Training is based on 3-games per week (Saturday, Tuesday, Thursday). Now that you are out of the cup, you want to schedule a scrimmage every week. There is no money involved, so it is all about training.
With 3 games, you can get 144 minutes at each position (48x3) so it is generally fairly easy to get two players at each position, and perhaps get some additional training for another player. While someone who plays 40 minutes will get less training than someone who plays 48 minutes, it is not known how much less. It is probably less than proportional (less than 40/48), but probably not useless.
I would generally start my best C and PF for both league games, and not worry too much that they are over 48 total. You also want to win games. If you have an easy game, you might consider using one as backup. If they are a lot better than your backups, they will still get plenty of playing time. Home games give you a boost to rebounding and inside defense, so if I were going to use the better C as the backup, it might happen at home.
Then in the scrimmage, don't play your best C and PF, since they already should have their 48 minutes, and they might get injured. You should be able to get your 2nd best players up to 48 minutes, and get some training for a couple of other players. You could either carry a 3rd C and PF, or you might think about playing one of SF at PF in the scrimmage. Rebounding and inside defense aren't going to hurt a SF.
You might also mix up the positions. If you train PF/C, a player who plays 28 minutes at PF and 20 minutes at C, gets just as much training as if he played 48 minutes at either position.
You probably don't want to stick to any particular skill more than a couple of weeks. Players need a combination of skills. While it may nice to have a skill is a bit better than the other skills, you don't want to have any that are significantly worse.
On the Staff menu, you can select a new coach. Each week beginnig on Monday a different coach is offered. So next week if you check, there might be a "4" offered; and then the following week a "10". So you have to keep watching to see what it available on any particular week.