I'd like to know that as well. I thought all progress would go into SA/New position unless you paused it. But I just received a skill point from a friend, it went to a player who I'm giving a new role, but I don't think it went to that new role (or SP gifts don't work anymore). At least I wouldn't pause it and keep an eye out for progress.
Also struggling with how to fit in GK training. Seems like it doesn't make sense to give GK training to other players, they don't have those skills. So GK training + 2 different Physical and Mental exercises for 2 GK's, would that work towards a bonus? Wouldn't progress be awfully slow?