Here is an exercise I made for myself in iReal Pro to do the ii-V-I in the cycle. 

I'm still struggling with it, but here are steps I'm making to get better.

1. I'm learning bite-sized arpeggios, so I can quickly see the Root, 3, 5 and 7 when I find a root.
2. I practice moving chords in fourths on the neck, figuring out the pattern.
3. I am doing a Maj9 arpeggio of 1, 9, 3, 5 starting on the G of the sixth string, saying 'G'.  Then I'm moving to the C on the 5 string and repeating the same arpeggio, saying 'C'. Then I move down to the F, then Bb, then the Eb (on the 4th fret now) and then Ab, saying all the names.  Now I go to the A on the sixth string at fret 5 and continue through the cycle, playing the 1, 9, 3, 5 and saying the Root.  Do this up the fretboard and back around.  Note that the 9 is really the ii.
4. Now when I play the exercise, I should start to recognize the movement of the roots, either backwards down the fretboard, or straight down towards string 1 and back up to six, going up the neck.
5. When I see the first chord of the ii-V-I (e.g. A-7) I find the root and call it a ii.  I realize the Root is a whole tone (two frets) down from the ii.  I also visualize where the 3 of the I is.  That is a good landing note for the I.  The b3 of the ii is really a 4th away from the root.  Eventually I'm starting to see the arpeggios, and, most-importantly, the 3s and 7s of the arpeggios of ii, V and I.  Start to find ways to memorize these relationships.  For instance, the b3 of the ii is also the b7 of the V.
6. You can also focus on the I, find that, and then visualize the ii a whole town up, with its b3 falling on the 4 of the I.
   
7. Try to anticipate where the next fourth is, either in terms of the ii or the I.
8. I cannot really escape those mode boxes, so I'm always visualizing those in terms of the roots.  For example, if I locate the A-7 on the second string (10th fret) I see the I7 will be a fret down, and at the 'tip' of the r6 Dorian scale shape.  That means that the ii is in the r6 Mixolydian box.  Eventually, I want to learn what box I am in if I call a note a 'ii' or a 'V' or a 'I'.

Another exercise I've started to do is play the whole cycle in one position.

If I'm playing A-7 as the ii on a r6 'Dorian' box,  I know where the G, its 3rd and its 7 is.  There is one on the second string, 7th fret.  I know the next 4th will be one string down, on the C.  That means the next 'box' will be r6 Aeolian.

The boxes basically cycle like this:

• Ionian - root of I on 6, 4
  
• Mixolydian - root of I on 5, 3
  
• Dorian - root of I on 4, 2
  
• Aeolian - root of I on 3, 1
• Phrygian - root of I on 2, 5

After Phrygian, it starts over again with Ioninan, but one fret up from the last Ionian.  Just like when I did the maj9 arpeggios in number 3 again.  You can try doing this exercise again, except instead of saying the root note, say the r6 mode box where the root is in: Ionian, Mixolydian, Dorian, Aeolian, Phrygrian.

If I'm playing the r6 Mixolydian box in F, instead of going down, I can work back to the r6 Ionian in Bb and keep working backward in Ionian, Mixolydian r6 boxes.

Mixolydian works back  and up to Ionian
Dorian works back and up to Mixolydian
Aeolian works back and up to Dorian
Phrygian works back and up to Aeolian.

According to Carol Kaye, most jazz soloing was developed in the forties and fifties off chords, not scales.

The chromatic, major, minor and other scales were used more as 'traveling notes' to get to essential tones and arpeggios.

I am making an effort to stop visualizing in scales and start visualizing arpeggios.  Take Cmaj, as played with C on the third fret of the 5th string.  I immediately recognize there is a box there shaped like the root-6 Mixolydian scale pattern.

But now I'm trying to learn how arpeggios sit in this 'box' for the 'ii' chord, the 'V' chord and the 'I' chord.

You can practice the diatonic sequence within this box, just using arpeggios.

Cmaj7 (I), D-7 (ii), E-7(iii), Fmaj7(IV), G-7 (vi), and B-7b5(vii).

The chart below shows the sequence within the root6 Mixolydian box.  Practice the arpeggios starting with the root and work your way through the sequence (I, ii, iii, IV, V, vi, vii).  Say out loud what chord you are going to play next (i.e. 'ii chord').  Then say the interval as you play each note of the arpeggio.  Also practice these arpeggios starting with the 7th interval moving in the diatonic sequence.

Once you know the arpeggios related to each other in a 'box', you can start playing with lines in a 2-5-1, visualizing each arpeggio within this box.  After that, move to another 'box', like the root6 Ionian box, and repeat the exercise -- playing arpeggios in the diatonic sequence.  Then play the arpeggios for a 2-5-1.

Once you have a good visual feel of the arpeggios and their intervals in a 2-5-1 sequence, try a 3-6-2-5-1 sequence.

Why did I stagger the sequence in the chart above so oddly?  Let's break down the diatonic sequence a little more.

The minor iii chord can substitute for a major I chord.  Play each of the arpeggios and listen for yourself.

Think of the iii minor as part of the I.  This is why the 3-6-2-5-1 works as a turnaround.  It starts on iii which is like starting on I, passing in 4ths on the cycle back to the I.

Similarly, the major IV, is part of the ii chord.

The vi chord is also part of the I one chord -- the arpeggio of vi7 works out to I6 -- a Major 6 chord.

The half-diminished vii can be thought of as a dom.9 chord.  A common guitar 2-5 is to play, say A-7 with the root on the bottom, then move the b7 a semi-tone down to create a D9 chord, which is essential the min7b5 vii chord of G.  Try playing the B-7b5 arpeggio over the D9 and you will hear.

In the chart above you can see these relationships horizontally.

You can also play a min7 arpeggio of the ii over the min7b5 arpeggio of the vii (e.g., A-7 over F-7b5).  The min7b5 chord is the 'ii' of a minor ii-V-i progression.

Learning this will help you see substitutions more clearly.  Whenever you have a minor, just think of it as a 'ii' chord.  That means you have a 'iii' minor a whole tone above that and a relative 'IV' major a semi-tone after that.  This is what Carol Kaye calls the 'slide rule' effect. 

You can 'reference your triads' to see what chords work over a change.  For instance, if you do your triads for G7 (start on the 6 string root), you work your way up and see that G7 works with D-, F, A-, C, E-, G, B-b5.   You can play D- over G7 -- think about the common vamp between the D-7 and a G9.

This chart shows the 'boxes' or scale patterns I typically visualize across the neck for a key.  Each box corresponds to a mode with the root on the sixth string.  If you don't know what a mode is, it is just the notes of a Major scale, but with the root on a different key.  For instance, Dorian is the major key scale if you use the second tone as the root.  Mixolydian is the mode if you use the fifth tone of the major scale as the root.

In the 'CAGED' method, each box also corresponds to an open chord fingering (and it's arpeggio).  For instance, the open C chord fits over the r6 Phrygian fingering (that starts on the 6th string).

I've also included the intervals to the I chord.  I used roman numerals for the ii and V to impress that these numbers are where the scales start for other chords in a diatonic (major) progression.* The ii-V-I is about the most important progression in jazz, so being able to visualize the relationship of these roots are key.  However, it extends to all the diatonic chords.  The root of the vi chord is always on the 6th tone.  You can see with the Aeolian mode (which starts on 6) that 'Aeolian' is a perfect scale to play over the vi chord.  Phrygian is the best mode to play over the iii chord, etc.

I also included the Locrian and Lydian modes, although I don't visualize them so much.  They are so close to the other fingerings, it is harder to distinguish which box you are in.  It is good to practice all modes to see how the sound, however. 

It is essential to know where the 7 is in the major scale however.  It is not only a 'guide tone' of a I7 chord, but it is the root of the vii chord - always a min7b5.  When you know all the intervallic relationships, you can quickly find a root based on the progression -- then position a chord and find the scalular notes or arpeggios.

*It is too unwieldy to use roman numerals throughout the chart because 'iv' and 'vi' get confusing.

Here are inversions for Dom.7, Maj7, Min7, Min7b5 and Dim.7.  They are stacked against each other so you can see how they relate to each other.  Practicing each fingering across will help ingrain what part of the chord each note is and where intervals sit in relation to each other.

I am back to learning arpeggios again, this time I'm focusing on just learning 4-note arpeggios, trying to "anchor" them to the diatonic 'boxes' I am thoroughly familiar with.  I'm practicing solos by quickly finding these arpeggios with each chord change and also visualizing the corresponding mode shape learned through the 'CAGED' method.

For songs with faster changes, there isn't time to play a two-octave arpeggio, so learning these 'bite-sized' versions let me nibble at a change before it's gone.

I'm using 'iiR5' to connote where the root of the 'ii' falls on the fifth string within the diatonic boxes I've memorized.  The box 'r6 Mixolydian' is a scale shape I visualize, a 'box' which is equivalent to the Mixolydian mode where the root is on the sixth string.  I know the 'boxes' for Ionian, Dorian, Phrygian, Mixolydian and Aeolian modes with a sixth-string root.  I learned these boxes through the CAGED method.

Part of my practice is playing an arpeggio and finding a corresponding mode 'box'.  As minor chords can either be the ii, iii or vi -- they correspond to different modes, and different 'anchors' on the diatonic boxes.

Another part of the practice is staying within a box and finding the ii and it's corresponding arpeggio.  Then find the V and I.

I made this chart to begin creating visual "anchors" to the diatonic modes I am already familiar with.

I've been practicing the Harmonic Minor, which I know serves as the Altered Scale when its root is on the b9 of a Dominant.

Now I need "anchor" it to the modes I already am familiar with, so switching to the Altered Scale will be instantaneous.  I'm practicing switching between each section of the Altered scale with the corresponding mode in the diagram, measure to measure.  Then I'm practicing a ii - V7alt - I progression to get to the scale in time.

I basically visualize 5 "boxes" which correspond to five modes where the root is on the 6th string.  The Lydian and Locrian are so close to the Phrygian and Ionian respectively that I just picture the later boxes.

I use 'r6 Aeolian' to connote the shape of the Aeolian mode where it starts on the sixth string.  I'm using 'Vr4' to connote the root, arpeggio or scale for the V (Dominant) of the diatonic progression where it appears on the fourth string.