Well you're not in the cup anymore so if you play them 35 minutes or so during both league games and rest them in your scrimmage you should be fine with game shape, and when you are in the cup you have to choose basically 2 games a week for a player to play in if they are playing high minutes. Sometimes to get further in the cup you have to lose a league game by more then you would of or maybe even lose one you would have won. What you should do is since your team is 3-3 you should have thrown the games to the teams that are better then you and saved some of your best players for the cup if you needed them.