Most Audis can have one to four (sometimes eight) keys coded to the immo. So the best way to do this, is to have all the keys you want coded at the same time, that way the shop/dealer can make sure that only these keys will work on your car...

 

In fact it has to be that way. All the keys that need to be set up and coded have to done all at once. You can't do them separately. It generates a new code on each run and old data doesn't carry over ... afaik ... and this is immo I'm talking about. Setting up the door locks can be done one by one but a master still needs to be present.