daz72

hi
I can't find much info on this, so thought I'd ask the experts (that would be you guys).

I recently got a Viper 5701 2-way remote start/alarm system installed in my '05 GT.
But the shop crew are having a tough time making it work properly. The remote start seems to be fine (which you would think is the hard part), but the problem is that the Viper still interferes with the factory security system.
They are using a bypass module, which they claim is the right one. It's one of the newer ones that needed 2 keys to program, but doesn't need to keep a key in it to work. (I didn't want the type that 'eats' a key)
Problem is that if I arm the Viper, leave the car, come back and disarm Viper, when I open the door the Ford security system goes off (horn honks etc). So clearly it's not being 'bypassed' correctly.

So my question is - how should this work if installed correctly. Should the Ford system basically be 'deactivated' and replaced by the Viper, or should they somehow work in combination with each other? Should I just be carrying around the Viper fob, or will I always need the Ford fob too? I don't want the car to end up easier to steal than it was to begin with...

thanks a lot guys
Daz
redwood city, ca