When you are training an SA, your player will not gain in any other skill. You can pause the training of the SA if you want to work on other skills. I generally train SAs on players. I have no idea if they actually help. I like to enhance a player's natural ability. For example, I'll give a good crosser the corner kick SA or a good passer the play maker SA. But that's just the way I do it. There is a lot of info on this forum about special abilities and if they're worth it.