yeah you can run them seperatly as i do with my logitech g27 and they are meant to work alot better using there seperate usb, are your fanatech drivers up to date, my game picked them straight away,
make sure once you have the pedal connected via usb that you go into the fanatec profiler and configure and calibrate the pedals so the profiler detects them as a seprate device
jeremy your love the csp there super build quality design, just so awsome take awhile to adapt too but once set up corretly there awsome,