yes you can, but honestly not sure if you want too.
http://www.autoblog.com/2010/03/25/forum-fodder-dealer-accidentally-remote-starts-customers-musta/
That is exactly what can/will happen if it isn't done right infact if you do a search on mustangforums-com you will see that he asked how to do the same thing and I warned him aginst it. Well he figured it out and thought he would always leave it in nuetral, always have the brake on, nobody drives his car, bla bla bla. That happend 4 months after. He threw a big fit and somehow got insurance to cover it even though he bypassed a factory installed safety device.
I have a remote start on my mustang and its a manual but this system(compustar) was designed to go in a manual. When I park the car, I have to hold the foot brake while I put on the parking brake and the system knows I am parking it, and its in nuetral and running. When I turn the key off, the motor actually keeps running(powered by the system now) until I shut my door. When the door shuts, it locks the door and arms the alarm and knows that the car is still in neutral. As long a the door triggers are not set off, it will know its still in nuetral and allow me to start it. But if I go and get back inside the car but do not start it, then it doesn't know its in nuetral and will not allow me to start it.