Depends on what you think sounds good. As a rule, the A scale will always work while you're in the key of A; but yeah, you could also experiment with the different chord shapes in that key (eg. pick some of the notes from the A chord while the rhythm plays it, then pick notes from the D chord when the rhythm switches to that chord). The only time you ever really need to switch root notes during a piece is when there's a key change.
Basically, the scale corresponding to the key you're in will always work within that key; but some intervals and notes in the scale will sound better than others.

Well, there you have the rules: now, if you wish, you may break them for the sake of the groove ;)