Please add a setting to disable automatic track assignment to hardware MIDI ports and allow ports to be enabled but hidden outside of the preferences dialog. If a control surface is using a port, the port should not be visible in the list and Sonar should never automatically assign a track to that port.
When a MIDI track is created, it should default to a (null) port. Port assignment should also work like bus assignment; if you have 12 MIDI tracks selected and do a Ctrl+Assign to a MIDI port, all of the selected tracks should follow.