Practice your progressions diatonically. That's what helped me out.
After a while, once you understand that, practice modes doing the same "mode" scale across each note of the diatonic, so if you're playing a Amin scale over a F chord (and you're in the key of F), then play a Bbmin, Cmin, Dmin, etc. scale over an F chord. Do the same with each mode, across each note of the diatonic. It may sound weird, but after a while, you're ears will start to open up to different possibilities.