Sorry your right. I'm thinking of the old install through root. The correct folder is /usr/lib/mupen64plus

Also finished or not I will be uploadinng my auto config script tonight. Basically simplifies a fair few steps for user ps3 controller, wiimote or accelemymote.

The issue I'd had so far is you need to be root to run it.. and typing sudo gainroot everytime is a pain in the neck. It works now as root but has to jump a couple of hoops to do so.