I'm sorry if I wasn't clear. I know what you are saying as I have a Viper 350 myself. You don't wire the rear door to the alarm itself. The popper kit, if you got it from Tone, has the solenoid, popper, and a pin switch. the wire from the pin switch goes to a wire located in the passenger door sill area that is connected to the ground wire connected to the side door pin switch and is very easy to do.
Here's his instructions in .pdf form.