I have a basic question about switching presets using a MIDI controller.  I am using a MorningStar MC6.

If you switch presets manually, the preset number flashes until you hit the 'Active' switch.  This engages the preset.  I am trying to do this thru MIDI.  The preset changes just fine BUT it automatically engages.  I would like to have it flash until I step on the 'Active' switch.

Well, if you use MIDI CCs to trigger incrementing or decrementing presets, you can either choose to have the presets increment (or decrement) and load automatically, or you can choose to have them increment (or decrement) and remain in the pending state.

You can configure this in H9 Control by going into Pedal Settings, going to MIDI Settings, and then to Assign MIDI CC messages to pedal functions.  You can configure it on the H9 itself as well;  the user manual describes in detail how to do so.