well I extensivly used pulse start for my system in the past.
First a clarification, what the carnetix receives the first pulse any subsequent pulses will have no effect for the duration of the boot lockout (or whatever its called) so the PC will start with the first pulse and the second (for your passenger door) will have no effect.
I had it connected to the unlock wire inside the drivers door. So when I hit unlock the PC would start. since you have the advantage that the rest of your doors need to clicks you can connect it to the passenger door unlock wire. So if you don't want the PC to start you click once, if you do then you click twice and initiate the boot(plus unlock all doors).
The shutdown in my case was and still is triggered by the ignition.
As an other more complex option you can use a device that you can program to accept a number of input pulses to output a single pulse. So use three clicks to trigger the PC. This was my initial plan. I actually think that I will be implementing this since having the PC booting EVERY time I unlocked the car once was a bit annoying so I had to disconnect it.