Well, sometimes its unavoidable when players foul out i suppose. But let me just say this, a good idea especially for scrimmages is, whomever you're training put your tactic to strickly follow the depth chart, say for examply you're training center.
Put the center you're training as your only center meaning, put him as the starter, backup and even the 3rd stringer. That's what i did with two of my players, and both of those players got 48 minutes tonight, you can check my game for tonight's cup game to see. I advise you to do this only in scrimages though and not league games.
Meaning only put your center or power forward that you are training as your starter, back up and third stringer. That's how i train players in scrimages. I've had players that fouled out to before they got their minutes. Maybe some other people have other ways that they train players that can help you out.