Probably best time to train stamina is weeks when you only have 1 league match and 1 scrim.
Those are All-star week and at the end of season when you drop out of play-off / relegation.
Usually these are weeks when if you have 3 trainees for single post training, you'll have to either sacrifice 1 of them or change your training plan anyway. Same goes if you have 6 trainees for 2 post training.
Also Stamina trains really fast and it trains on everyone whether they played 48 mins or not.
You might get 3 weeks (maybe 4 sorry math and dates...) like this in a season, so in 2 seasons you'll have plenty of stamina on whole roster