Your welcome.
I don't know about FL Studios possibilities.
But If you in B3 V2 have set the upper manual to respond to midi channel x, the lower manual to midi channel y, and the pedals to midi channel z, then the rest is about how you route midi in FL Studio.
In many B3 V2 presets the upper manual is allready set to respond to midi channel 1, the lower manual to midi channel 2, and the pedals to midi channel 3.
In my DAW Studio one i have to use a track for each manual/ midi channel routing. So i use 3 tracks that's assigned to the same B3 V2 plugin.
In studio one Arturias plugins unfortunately have to be the VST2 versions to do this.
I can in example also selct a certain controller to control a certain track in my DAW.
If you don't know how to do this routing in FL Studio, then i suggest you ask about that in FL Studio forum. It's the same for any plugin, that can recieve on multiple midi channels at the same time.