Viper 791XV on Dodge Intrepid

I have a 2000 Dodge Intrepid and I hooked the Viper up on it, and everything works fine, but when I turn off the car or my remote start the windows still roll down with out the key in and my A/C and heat can still be operated, basically my accessories stay on, what may be the problem.

Also how would i go about adding two extra L.E.D.'s to the alarm I tried to use the existing one to parralell it but it didn't work for me, does anyone have a clue.

                          Deezy