1. Basically you want 48 minutes for players that are training. Therefore, keep your best team on the floor for those two real games and put your lesser trainees in the scrimmage. Overall, you want your trainees to get at least 48 minutes to optimize your training. Sometimes this doesn't work out since you want to win games as well, but you'll be able to address that as time goes on.
2. You should treat training based on position. So you can train guards, small forwards, or center/power forwards. So if you train C/PF you have 6 potential training spots to fill the 48 minutes (though this is really hard to do, you will most likely get 4 trainees to get 48 minutes). The best trainees are obviously the youngest ages of 18/19 but players train well up to about 24.
3. DO NOT TRAIN ONLY ONE SKILL. This is very important. You can look in the help section and that will tell you the most beneficial skills for each position. Therefore if you train C/PF you should rotate skills between IS, ID, RB, and SB.
That's about all I can come up with at the moment. Now I must leave to drink many a beer.