Without seeing how good both players are I can't say what is best but you run a serious, serious risk of injury or foul trouble crippling your team if you don't have back ups (the coach will replace the injured/fouled out player with someone... but it rarely is the person you would want).
If you think there's a huge disparity between your starter and back up you can put the starter at Starter and Back Up and put his replacement at Reserve. The reserve will still probably get minutes but not a ton. (I am not 100% sure of how this works, though).
If you have two very good guards and one decent backup guard you could also have the same player play Back Up SG and PG which would keep both starters in the game for much longer.
Personally I would make sure to have back ups in place during the playoffs at all times. Playing 48 minutes is really only a smart thing to do for training purposes, not winning purposes.