To setup HDHomeRun devices:

Each HDHomeRun device is setup as a single source in Virtual Matrix.  HDHomeRun Prime can support 3 simultaneous streams per device, so if you need more than that you can purchase multiple HDHomeRun devices (and setup one source per device).

Selecting the active channel number to stream requires using the SETCHAN protocol commands (or the appropriate driver).

You can also setup individual channel to tune directly as VM source