I've been single position training three guards, and in order to consistently get their full game in, I do the following depth chart
starting - backup - reserve
PG Trainee 1 Trainee 1 Trainee 1
SG starting SG backup SG backup SG
SF starting SF backup SF backup SF
PF starting PF backup PF backup PF
C starting C backup c backup C
Strictly follow and let them play for substitution and foul trouble choices.
This will help prevent weird substitutions if you have big blowout wins.
But, if you're trying to get 48+ min for three players in single position, there's nothing you can do if you suffer and injury or a foul out. That's part of the risk of doing single position training, in that when that happens, it becomes very hard to win your game.
In weeks where you have a game where your trainee doesn't get his full 48+, you'll have to decide whether to switch to two position training (in which case you'll want to plan beforehand what you would switch to, and where you should be playing your other trainees as backups), or just bit the bullet and accept the sub 48+ minute on your unlucky trainee.