OK I installed the remote starter and that portion of the unit is working well, the problem is that I cannot use the factory alarm. If I set the alarm and use the aftermarket remote to open the doors the alarm goes off. Also if I lock the doors with the aftermarket remote the alarm will not set. There is a remote disarm and arm wire from the unit, but I am not sure what wire to connect them to, I have a FSM, and cannot find the wire to do the trick... Any help is greatly appreciated..

Do you want to have both, or do you just want the aftermarket?

In a perfect world I would like ot have both, meaning being able to lock and set the alarm with the aftermarket remote but I would settle for just disarming the alarm.

what brand of aftermarket alarm are you using? I think the first thing I would try is to program your aftermarket alarm remote to the Nissan alarm.

Its worth a shot. Here are directions, make sure you lock the doors with the switch once you are inside after step 1:
http://www.xterraparts.com/html/instruct/remote.html

I got it working, I had to use the signal from the key cylinder so that now with the aftermarket remote I can unlock and lock the doors which at the same time is arming and disarming the factory alarm. So now I dont have to use two remotes... Thanks..

cool, glad you got it worked out.