There should be a blue wire in the drivers door that is the factory disarm wire. you will need to test this wire using a multimeter, if you are not familiar with a meter then you can take it back to the dealership or place where the aftermarket alarm was installed. once this wire is located, ground the wire and this will keep your factory alarm disarmed. also find the fuse for the aftermarket alarm as totalimmortal suggested and remove.

this will disarm both systems rendering your problem.