FastBikerBoy: MIDI Omni should sort that out, or if you prefer not to go the omni route use the MIDI input presets feature. Select "Manage presets" from the input drop down and assign input ports/channels as required.
FastBikerBoy: If you use "MIDI learn" to assign pads to cells it should only respond to the assigned cell, not sure what is going on there if it is responding to all incoming MIDI. I'm a little confused by what you mean. DO you mean if you press a key on the PCR every matrix cell responds? Just one? You can set which channel the matrix responds to using the icon towards the top left of that view but unless specifically assigned a cell shouldn't respond anyway.
I've set up one of the control maps on the PCR to assign the pads to notes rather than CC. With the default Sonar map it is mapped to work with ACT, so if I assign a cell in the matrix to a pad, hitting that pad would also trigger a function via ACT, which is less than ideal. Hence I have a map for ACT and one where the pads are assigned to notes.
I've put the soft synth to listen to the PCR-1 midi-port on Omni, but I can't choose what midi-port the Matrix should listen too, only which midi track. And it appears the matrix is listening to all midi-ports. I can use "manage presets" for the tracks, but that doesn't solve the problem as the cells in matrix listens to all midi-ports. At least I can't find the setting for the matrix to only listen to midi-port PCR-2.
So what happens is that when I play the pads with the setup explained above, the matrix responds as it should and the soft synth is silent, as it should. It is when I play the keyboard the problem occurs. Then the soft synth plays as it should but it also triggers cells in the matrix if a cell is assigned to that particular note.
If I was able to find the midi-port selector for the matrix, it would be so much easier. I could just switch controller maps on the PCR depending on if I wanted to control ACT or the matrix.
If I have a second pad controller, say a Novation Launchpad and wanted to trigger cells from that, I still can find a way to tell the matrix to only listen to the midi-port Novation Launchpad.
The bottom line question is: where is the midi-port assignment for the matrix?