Hey Gents,
What I did was to make a new folder called 'Altered airports', put a scenery folder in it and then placed the new bgls into that folder. Then I added them in the scenery library within FS and that was it. As I mentioned elsewhere, all it adds are some waypoints to FS.
This way, if there's any conflict with your system (I can't imagine why there would be), you can easily isolate the files and/or remove them.