If you look at the literature, two things can help migratory species. First is the size of the MPA. For it to be effective, the MPA has to be large, fortunately or unfortunately. That can lead to other issues but you need to cover as much of their range as possible for it to be useful.
Second is the new research that has just been published by Sally Otto, Daniel Pauly, and others, where they look at fish behaviour. It's amazing. They found out that fish evolve also. If you have an MPA and they know it's an MPA when they're in there because no trawling is chasing their shadows, and so on, they learn to be within the MPA rather than going to another place where they will get smacked. So they are not as stupid as we think they are.
This is new, quite cool research. After some time, they stay more in the peaceful areas than in the crazy places where they get hit. There's a lot of research coming out on this still.