That's a little bit tricky.
I've dealt with an aftermarket alarm before. Fortunately for me, I was able to rip it out no problem. Lots of recripping/soldering wires back together. The idiot before me used scotch packing tape to hold the little Viper brand security system unit up under the dash. He just kind of wrapped the tape and box around a bunch of random wires...
What you need to do is, follow all the wires to where they're attached to and disconnect them all that lead back to the aftermarket security system box ( under the dash I presume). The wires running from the box should look clearly different from any stock wiring and will all lead to different things like a door chimer, headlights, key on, things of that sort. Anyways, these aftermarket wires
should be simple to remove without causing any side effects to your original factory harness
While looking over the aftermarket harness of the security system just look for the simple things that could impede any original connections, splice ins (which you should remove), cut stock wires that could be now linked to the AF security system.
There's not much wrong you can do as long as you take your time and examine where everything goes.