First and foremost, with Yamaha, the multi-pad is attached and directly associated with the style file. Therefore, when you select that particular style, you automatically select the attached multi-pad. Now you have a couple options:
1. You could change the multi-pad of the style file, then save the style as a custom style and every time it is accessed, the new multi-pad would come up with the style.
2. You could also save the information to a registration, but if you were to change style variations during a song, the multi-pad would revert to the default multi-pad. Therefore, you would have to make all your changes through registrations in order to avoid this problem.
Personally, I would go for option #1, and I would rename the style file to the song title. Makes life a lot easier.
Gary