Do .cfg and .air file need to be in agreement ?


I've been playing around with Aired and note book and comparing the .air files and the aircraft files and note that there are usually some (and sometimes a lot of) differences between these two files.
Just how do they interact with each other and in the case of a difference between them which takes priority ?
When two men ride a horse one has to ride in front - so which one of these files rides in front ?