How long is the control pod cable? Can it sit on top of the desk while the sub is on the floor?

The cable is quite short; not sure of the exact length, but definitely less than 5 feet. You might be able to put the sub on the floor, but you'll have to stretch the other wires to their limits. I get the impression the intended setup is for the PC, sub, both speakers, and the control pod to all rest atop the desk.