Factory Alarm with Aftermarket?

[truthchild]

Okie Dokie, so it all started last night in the cold of course. First off its a 91 xj limited of course and it has a factory alarm system, well when i purchased this vehicle a while back they didn't have the remotes for the Jeep so i didn't bother. Well long story short I decided to have an alarm system/remote start installed due to activity around my car and my rear liscense plate gone missing. Coming out to my car last night i use my remote to disarm the alarm, my aftermarket Clifford Matrix RS2 alarm disarms with the chirp chirp, but the factory goes off which i have never heard before (wow put my aftermarket to shame for sound, lol). You all are probably wondering I have seen posts about this and have read how to disable the factory alarm. Well heres why, the people that installed the aftermarket wired into the factory one, why i don't know but they did. FYI if you live in Colorado Springs never go to Drive in Autosound they will try to screw you whenever/where ever and they do crap work on installs (not only happened to me but also a Doc I work for). So comes the question, will i still be able to have my aftermarket alarm work if i disable the factory since they are wired together, and will i have screwed myself since all i did was disconnect the battery to turn off the honking and flashing lights then unplugged the factory security modual and reconnect the battery? Also attached with this problem is now that my factory alarm has gone off and is disconnected I am unable to start my car, the starter kicks the engine over and the fuel pump is on but it will not catch to a start. Could this be because i disconnected the factory alarm? Thanks for the Help guys.

Drew
91 XJ limited