Thanks for reading this I hope I describe what I need correctly but if not please show patience
I just bought a Hammond VK3C Pro dual keyboard organ which transmits midi (Ch)1 top keyboard (CH2) bottom keyboard and (Ch3) pedals. I set up 3 midi input on CUbase 6.5 for input (CH1-3). When I trigger each individual keyboard and also pedal it records to all tracks (1-3) simultaneously. The Organ itself is set to transmit on correct channels so I assume that I have to create some kind of filter to make each channel that is record enabled respond to correct Midi channel. Can anyone point me in right direction, I reached a point of frustration and before I reach for the big hammer thought I’d reach out for help 
… Just add a local Input Transformer to each of the three MIDI tracks, and, for each, filter out all but the desired MIDI channel. There are already Input Transformer presets for doing the job (in the “Channel Filtering” subfolder).