Well whenever you come accrosst a certain chord, those are the scales you can pick from to play over that chord. i.e. Say you see a Bm7b5 chord, well just play a B locrian mode over it. And if you understand how modes exist within the major scales, you can see what chords work within a certain major scale (key signature) i.e. "I" is Ionian, so "II" is Dorian, and so on. So if you have a tune in the key of E major, E is the "I" (Ionian), F# would be "II" (Dorian). So in the key of E major, F# could be played as a minor 7th chord and the F# Dorian is good scale to play over that chord.