Well I looked at your chords
Cmaj/A: A C E G or A minor 7th
BMaj/A: A B D# F# or B Dominant 7th with A in the Bass
and then looked at the notes and said well the only scale that has these notes that are relative to both chords would be
E harmonic minor which is E, F#, G, A, B, C, D#
or looking at it from A you have A, B, C, D#, E, F#, G which is Dorian #4.
Well when applying this to the chords I would emphasize the chord tones within the scale and use the other notes as passing tones
when looking at your progression when transitioning
A stays at A
C goes to B
E goes to D#
G goes to F#
So all the notes move down a half step so when you transition from one chord to the next I would emphasize one of these half step movements,
Like say first time say your going to target the E to D# half step than on the next pass use one of the others and so on for starters.
Hope this sheds some light on the subject.