If you are training players, never let the coach decide. Always choose "strictly follow depth chart." and then if you are doing one position training, say point guard, for the first game you set the first player you want to train at "starter" "reserve" and "backup" that way he will get 48 minutes for that game, then you do the same for the next two games with the other two players.
As for controlling playing time for other players. You kinda have to get a feel for how many minutes a player will play per game. Ususally a starter will play 30-40 minutes per game unless it is a blow out then the reserves will come in for most of the 4th quarter.
I usually plan on my starters playing 30 minutes for my two league games so they get their 60-70 minutes and then I use the cup/scrimmage to make sure my bench players get their minutes.