That setting is only for CPU controlled teams. You can Manually or Auto progress your own players anytime you want. I recommend putting that setting on four weeks or season so the CPU saves enough XP to get valuable attributes. Auto progress for your own players works reasonable enough to use but I personally like to do it manually.
Some tests I did today
http://www.operationsports.com/forum...d.php?t=574070
Formation subs must be done manually each game from the playcalling screen while the play clock is counting down. You cannot do it from outside the game and its quite cumbersome