I see. Well, I can tell you how I have mine setup, but it's very specific to my DAW of choice, Reaper.
One of the many cool things about Reaper is that you can develop your own filters using a variant of ECMAScript. When I first switched over to BFD2, I wrote a small filter that converts CCs over to Note messages. This allows me to effectively remap CC#64 over to Note#127, which I've then mapped within BFD to a cymbal choke group.
Again, that's very specific to my own needs, but it might give you some ideas.
BTW, that filter I wrote is also available here, should anyone also be using Reaper: http://nebiru.com/drumWagon/page.cfm/ReaperJS