I think what you are looking for is know the chord spelling of your chords, i.e. get chord names into interval numbers:
- C chord = R-3-5 interval of the C scale. And the D major chord is the R-3-5 intervals of the D major scale.
- Cmaj7 chord = R-3-5-7 interval numbers of the C scale. Yep the Dmaj7 is going to be the R-3-5-7 intervals of the D major scale. Place your major scale box pattern on the root note and the box will automatic place the right intervals (notes) under your fingers. Yes you will have to memorize where the intervals are within the box.
- Cm chord would be R-b3-5. Minor chords will always have a flatted 3 or b3.
- C7 chord = R-3-5-b7. It's a major dominant seventh chord so it has a natural 3 and the b7.
- Cm7 chord = R-b3-5-b7 Yes it's a minor chord and minor sevenths also have the b7.
- Cm7b5 chord = R-b3-b5-b7 This is a diminished chord and it has a bunch of flatted intervals.
- etc. etc.
http://www.smithfowler.org/music/Chord_Formulas.htm
Then take that to your major scale box.
Major scale box with interval numbers shown
G-|----|--2-|----|--3-|--4-|----|----|
D-|----|--6-|----|--7-|--8-|----|----|
A-|----|--3-|--4-|----|--5-|----|----|
E-|----|-----|-R-|----|--2-|----|----|
Fake chord has the C chord. Place the box's root on a C note on your fretboard and then play the R-3-5 intervals of the box. You just played the chord tone bass line for the C chord. Next chord is an F. Place the box's root over an F note and play the R-3-5 intervals of that box.
Notice if you find that first C chord on the 3rd string where will your F note be for the F chord? Yep, and how about the G note for the G chord where will it be? Piece of cake.
Want to place the root on the 3rd string of your fretboard -- just move the entire box pattern up a string.
Notice if you know where the notes are on the 3rd and 4th string of your fretboard you will be able to then place your major scale box pattern - on the 3rd or 4th string and be able to, using the box pattern, play any chord or scale you like. All you need is the intervals used in those chords or scales.
You talked about modes. C Dorian. Place the major scale box pattern - root note on C then play these box intervals; 1, 2, b3, 4, 5, 6, b7. you just played C Dorian. Want C Mixolydian? Play these box intervals; 1, 2, 3, 4, 5, 6, b7. You'll find the other mode interval sequences in the following.
http://www.dummies.com/how-to/conten...eat-sheet.html
Have fun.