Have you checked any fuses yet? I'd check all the fuses, replace any that were blown, then see how it goes. It could be that the wiring for the aftermarket stuff somehow got shorted out, and worst case might need to redone/replaced.

If you get stuck, you could go to a reputable audio/security installer and have them remove the current aftermarket security system and install a new one or if it's obvious what's wront perhaps they can fix it.