Heres the situation that came up in my last game. I set my pinch hitting to very aggressive since I have some good hitters on the bench. Late in the game, my CF1 came on to PH for SS2. Next at bat SS1 came on to PH for CF2. Theres no players left on bench. Next inning, SS1 stay on to play CF and CF1 stay on to play at SS. Is there anyway I can flip flop their positions in the future because I do not want that CF play SS ever again ? Thanks

CF1 : number 1 CF who's on rest against weaker opponent
SS1 : same as above
CF2 and SS2 : back up Guys who started the game to rest the starter

Odds are SS1 was in your defensive replacement slot as a CF. Take him out if you always rest both at the same time. 

As it stands, I don't think the PH/defensive logic can handle the situation you mention.

I also hate that situation as I do use my bench liberally.