If you're training 1 position and want to get 1 player 48 minutes, only select a 9 player squad with the trainee obviously getting the starter, backup and reserve position spots and the other positions set up as normal with your regular starter/backup rotation.
If it's just a gameshape issue, a blowout helps because you can play your regular starters for both league games and they'll get about 70 minutes as opposed to 80 or so if there was no blowout game for the week.
That seems to work for me anyway but i do have a doctor with massage skill too to help out when the minutes get a little high.