When you play the games it doesn't matter what the training is set to.
It matters when the training update happens. (I think its 6am EST Friday)
Always always always check Thursday night on your "manage my team" page (upper left long menu) and it will show the players that will be trained in the morning. For 1 position training, you can have 3 players max with "48+" showing and for 2 position training, 6 players max with 48+ showing.