Well, I don't know how you are set up at the moment, but when I had both a joystick and a mouse set up with X, I used xsetpointer to switch between the two. I think it's an XInput utility. update no, I don't think that this is a cross-platform solution that works with win32.

As far as a touchpad goes, I meant to replace the mouse with another touchpad, so that you'd have two (keep the laptop's internal touchpad turned off.) It's a little wasteful, yes, but touchpads have no drift.