[Qsilver7]

If you have 2 batteries...when you disconnect the main battery, the aux battery is still powered so be careful. If you do not want anything powered, then remove the negative terminal from BOTH batteries.

Ditto the post above, you won't need to "code" the batteries just because they were disconnected. But you may need to reinitialize some things around the vehicle...one of those things is the sunroof. You'll probably need to do a reset (push up & hold the sunroof button until it runs through its cycle...this info is in the owners manual). You may also need to reset the clock (depending on how long the batteries are disconnected).