The chord progression is what mainly determines which scales should you use ... Some chord progressions offers you wider range of scales , other do not.
i.e. If you have a prog like : Am , Dm , Am ... It resolves into an Am/Cmaj key , so normaly you'd go to play A minor (aeolian) mode but you can still play A harmonic minor over it too.
If you added a G#maj for example , you wouldn't play A minor since it doesn't include a G# , and you'd probably stick with the A harmonic minor instead since it has the #7th G#.
Usualy , as you increase the number of different chords in your progression , you narrow the choices of using different scales .
If you play an Amin chord only ... You can play A aeolian , phrygian , harmonic minor , pentatonic , or any minor scale that resolve into A.
Anyway, don't lock yourself into these , you can always include some accidental notes and dissonance as long as it appeals to you.
Your ear is your judge.