You might want to take a trip down to your local Electronics supply store (NOT RADIO SHACK, real electronics) and look for a 3-way SPDT switch that you can install between your ACC line and the M1-ATX. Install the switch on the ACC line going into the shutdown controller. I don't recommend using a momentary switch, I got mine specifically for my tablet but should work with a shutdown controller also. Just make sure the switch breaks the connection before making the next, i.e., completely isolates inputs.
Mine has labels ON-OFF-AUTO and I have it wired to my power supply with constant 12V for on and ACC for auto. This switch allows me to keep the carputer on always (ON), leave it off always (OFF), or let the shutdown controller do its thing (AUTO).