I'm pretty brand new to Inkscape. I've only been using it for about a week now. I'm creating a 2d video game sprite who will be animated in a program called Spriter. Spriter requires all of the body parts to be individual PNG files. So I have her upper arms, upper legs, torso, pelvis, neck, head, etc. Later there will be variations on those as well. ^ ^
My problem is that I've made quite a few shapes as paths, colored them all and then decided I wanted them to be combined into one. For example making all the individual parts of the eye (iris, sclera, pupil, highlights)-- and wanting to later combine them into one object with all the colors they had originally. However, when I use "Union" or "Combine", it makes the whole thing one color and deforms it.

Above is an imgur link to a largely unfinished shot of my character's face. The eye and all it's pieces are currently a group and I'd love it all to just be one path. Same with the flower, which is several separately gradient-filled objects grouped together.
Any ideas? Am I just missing something?
-Eva