mMaya is a great toolkit for importing large molecules like proteins, but I suspect it won't easily allow the granular control ShamanicHarmonics (?) is looking for as a new user. mMaya commandeers the nParticle system to create ball and stick models and I imagine it would be very tricky to create your own molecules.

I think maybe some basic parenting, constraining, and transforming tutorials are what's needed. Changing pivot points, duplicating with transforms, that sort of thing. It depends on the size, complexity, and purpose of the molecule.