For three position training I put in one player at the position at all three roster spots (starter, back up, reserve) and only dress nine players (all eight of the other players have a spot on both sub and reserve in addition in the starters being in the starting place) and I play strictly follow and let them play. I very rarely have problems getting them the minutes they need to get full training, but when I do I make sure that my main trainee is trained before the scrimmage so I can put him in as back up in the scrimmage to push him over 48 if there was an issue.
You run the risk of not choosing your sub if the trainee gets injured, but it's a risk you need to take to try to maximize training.
It's easy to get five players full minutes on two position training (and you can do six if you don't prioritize winning), but it can be helpful in all circumstances to slow down the pace of the game if you are likely to blow out the other team (or get blown out), so you can delay the coach going to the bench when the score gets high.