One of the things you might want to look into when you're compositing is rendering in layers. If you render in layers then you can work with each element of the character/scene independantly like say if you wanted to adjust character color without effecting anything else.

I'm not sure how to fix your problem I would have to see everything you're working with in front of me =/

but try rendering in layers in maya first then bring them into photoshop to composite them....