I actually had the same set up, but an Ampeg 810 instead. Try running the the RBI into the pre amp in on the 3 Pro, that way you will completely bypasss the pre amp on the 3 pro. No sense in running 2 pre amps. Never had any noise issues running it that way.
EX.: Bass > RBI input > RBI out into 3 Pro pre amp in
I think you get the idea. And this way is saves you a little bit of cash before the holidays.
Nowadays I just run a Shuttle 6.0 into the 810.