Create a custom playbook and make the substitutions in each formation. Or try this: start a game, and then go to the in-game sub screen. Make the substitutions, then quit the game and save the roster. Start the game up and check to see if the substitutions stuck. This will permanently change your roster – you can’t go back after. If you use a custom playbook option, it won’t permanently affect your rosters if you ever want to go back to the way it was.
Also, with Finn’s roster editor and Action Replay, you can switch ratings and positions for any player, even in franchise mode.