It is essential at some point to be able to visualize your intervals across the fretboard given a root note. In learning this, I quickly realize that, unless the notes are separated by the string shift at the B-string, the 5 always sits over the Root, the b7 always sits over the b3, the Root always sits over the 11, etc.
After that, I began to realize that since traditional positions move in fourths, and the guitar is more-or-less tuned in fourths, the 3-6-2-5-1 sit on each other vertically.
Here is the complete vertical layout of the intervals following this concept. Maybe it will help you learn the intervals, or at least be able to quickly double-check.