Yeah and I do this every time.
1) When the VIP option comes up and asks you to select your favorite team, select the team that you're going to be playing with in franchise.
2) Load the roster that you want to use in franchise.
3) Select a quick game with the team you just selected as your favorite team as both the home and away teams.
4) After the intro and while at the coin toss, pause the game and set the auto-subs to where you want them to be for both the home and away sides. You can also setup the "injury status" as well.
5) When you're finished, resume the game and then pause the game again and quit.
6) You should now be on the main menu. Start a franchise with your VIP/favorite team. And if you turn VIP to "none", the auto subs will still be what you just set them up as so dont worry.
7) Once in franchise, do whatever it is you normally do (weekly prep, play, etc.) and well, thats it. You're good to go. Personally, once I start the franchise, I turn pre-season back on and save the franchise.
There you go bud.