Here is what I did. I bought an Ernie Ball Neck Writting Papers book(like a tab book but pictures of guitar necks). I dotted in each scale. I found it preferrable to go in order of increasing sharps. That is do the C major(also A minor) scale first(has no sharps). Then the G(has an F#) and so forth.
When you learn this one scale, you've learned seven different scales on the whole neck. the C ionian(major scale), D dorian, E phrygian, F lydian, G mixolydian, A aolian(minor scale) and b locrian.
So when you go through this process for every scale(12) you'll know all the major, minor and modes. Also the pentatonics are inside of these scales, but no half steps. I find it best to learn the pentatonics seperately(even the box forms are ok on these).
I've fouhd using this approach of learning the whole neck like this, you can instantly play in any key without thought of this or that box, how the boxes connect etc... This has worked perfectly for me. I suggest, say take the C major scale, learn the first position first(first 4 frets). Then add the second position(while still using the first and second together). Then the third position(while also using the first and second as well). After that you've learned up to the 12th fret, it just repeats from there.