Okay, I know how to program a remote, but I have a 97 SE and 96 GLE, two keypads which are both programmed to the GLE. I took one of the keypads and programmed it to the SE, now it opens and closes both cars???

How do you program the SE so it works independantly from the GLE? Thanks for your help.

 

You program the car's ECU for the key. Not the key for the car! Therefore you can have one remote do 2 cars, both cars know the code of one remote. I think I read a thread on here that tells you how to clear all remotes from the cars ECU. Then all you need to do is program one remote into only one car. Check the FAQ's section on here I believe thats where I read it.
Good luck!