Maybe you can add an option where the user can choose at which airport he is, in situations where airports are very close.
No, that would be cumbersome, it's best to have the proper ranges specified, so you won't have to choose anything, it will just work on the smaller airport if you are inside its smaller range, and on the larger one if your are outside the range of the smaller one but inside the range of the larger.
As I've said, initially we must add support for these special cases, future updates might add an user interface to indicate the range of an airport inside an airport.