Well, to some degree I've gotten Fusion up and working with GameEx...it at least starts the emulator, then you choose the rom. I'm sure it's a command path problem, but don't know what I need.
As far as doing the shell thing, I just saw exiges' wonderful explanation of the same a few posts below this and it looks brilliant and well thought out. I'll just go follow it. Thanks guys!
This is the title of exiges excellent article=> Summary: Hiding XP / Booting to your Emulator / Optimizing boot