Not quite sure what the problem is? When soloing over a simple chord progression such as G to D, do you play a G phrygian scale or a B phrygian scale?
If you use a B phrygian scale do you actually resolve your phrases on the note B or just use the fingrering within that scale shape to improvise?
If you just use the fingering within that pattern to improvise melodies then you have no dependancy problem, because basically your just soloing within the G major scale.
To get better aquanted with the sounds of each mode try singing them while you practice, when you get to the point where you can sing them correctly without playing along then you know you have them in your ear.
Good Luck!!