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.
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 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.