Character with multiple wardrobes

Good evening,
I have a character with two sets of cloths rigged to the same armature as the character and works well in its file anyway. The cloths are on different layers for different scenes. I see that Sintel is set up similar to this but have not exactly figured out how they are used in different scenes, it looks like only one set has an armature modifire where both of mine do at the same time.
I am wondering if anyone has experience with this. I did not want to get to far into animating and find it has future problems. My movie is an hour long feature and that would be alot of rework.
Thanks,
Scooter