Well even the angstrom repository can bork things up if your not careful. FYI there is just about enough storage internally on the Pandora just to install an Operating System and supporting programs.. So it's best to just put programs on SD cards
If for some reason you don't want to use your SD card at the same time as your USB drive, you can run Panplayer from the USB drive in exactly the same way as you would on an SD.
You just need to create the same folder structure on the USB drive as you do for your SD, & place panplayer in apps or menu as desired.