how do you know wich scale to choose to improvise with over a certain?

Like Am7 chord tones are A,C,E,G

So you 'could' choose A minor, A dorian, A phrygian, i dont know what else,

so how do you go about choosing the right scale?
whatever suits the style of music your wanting
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it all depends on the sounds you want to put out.
Using any A minor scale would sound good over that chord, but each one has its own traits. Play around with them all and find out which one you like the best.
Well, it depends on the situation. If tha Am is in the key of C major, then A aeolian minor soudns best. If the Am is in the key of G major, A dorian sounds best. If it is in the key of F major, A phrygian sounds best. Why? becasue A aeolian= C major; A dorian= G major; A phrygian = F major, and you always want to stay in the right key...
there is no "right" scale to use unless you're interested in Pitch Axis Theory, which is in a nutshell using the mode that relates to the chord you're using i.e. in the key of C major -

C major - C Ionian
D minor - D Dorian

and so on
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