I'll have to double check, but I'm pretty sure you can designate one, or more of the upper sounds to the sub outs, so if you keep your organs in RH3, for example, you can run it through outboard gear, and have independent control. A good suggestion might me this:
Upper 1 - piano - main outs
Upper 2 - strngs - main outs
Upper 3 - organs - sub 1&2