As long as they are assigned to the team in your Create A Player menu (click on the player name, and hit "Assign Team,") they will be assigned in Franchise Mode as well.
I have noticed a couple of cases where players simply don't get assigned and wind up in Free Agency due to the fact the team didn't have any roster spots (example, Toronto Maple Leafs couldn't take on Aaltonen because Lupul and Horton were there.) So watch out for that!