Ehhh... Don't use geometric clothing... That's going to be PAINFUL. There's no sense in it. Plus, it will end up looking terrible. That is, unless you have some sort of soft-body physics engine, fluid/cloth dynamics engine, etc... And those aren't going to work with any degree of acceptable performance to get the desired effect (even if you had them).

I think you need to build in one "master" set of clothing to the models geometry, and rig it just like any other. The deformation of the body and clothing shall be one. You simply swap textures, and use shaders to get the realistic appearance, and make it mimic different types of cloth/material. That's the way it's done in games like GTA where you can buy new outfits and change clothes. I bet the Sims does the same thing. Everyone I know who has done something similar has just used texture tricks and special shaders.

I've, personally, never had a reason to do it myself, other than the code on the other end (HLSL and C/C++/C#). That's more of an "artsy" thing that other people do for me. I think your real problem will be "building in" a set of master clothing, since you've built the raw human anatomy. I've rarely seen that done for games. We don't do it either. We just build soldiers with the "base" of the uniform as a part of them. 'Add-ons' like helmets, weapons, etc are the only things that are really separate.