I wouldn't create sub-"projects"... keep everything in one project in one maya project. You can make subfolders in the scenes folder, and subfolders in the textures folder, but don't change the project for different parts, so you have to "set project". Hope that helps.

Edit: Maybe I misunderstood... anyway, don't change the "set project" for different subfolders, just navigate where you have to within your project using the browse window when opening and saving.