I recently took the trunk pop solenoid ("motor") from my '90 beater SHO to put in the wife's Civic.
The Honda already had a remote start unit (audiovox APS-685), which has a channel 3 output similar to your alarm, I'd imagine. There are some considerations to be made, though, for hooking this output to the trunk solenoid:
The trunk solenoid is a high-current device, drawing about 14 amps at 12 volts. Most likely, your alarm isn't designed to provide this much current through the auxiliary channel (CH3). Mine was limited to something like 0.5 Amps. The solution is to have the CH3 output energize an automotive relay, which switches the large current.
The instruction manual for your alarm should have a diagram showing how to connect a trunk solenoid. If not, let me know and I'd be happy to help you out with the details.
It's pretty easy, just gotta be wary that it draws a fair amout of current, so choose your wiring accordingly. I used 14 gauge, because I had that laying around. 16 ga should be ok too.
Nathan