Probably a dumb question, but......I have some waypoints ready to insert into an airport I modified with AFCAD. Do I have to edit the original AP9xxxxx.bgl file to place the waypoints, or can I edit the BGL file for the modified airport?

Don't edit the original stock file. Either create a separate bgl file for the waypoints or add them into the AFCAD file. Be aware though that AFCAD strips out certain information from files and does not allow approach data actually in the AFCAD file so a separate file might be safer in case you want to modify things in AFCAD

Since we are discussing the "terminal waypoints", if you define it as such within the airport element in XML code, then it will move a default terminal waypoint of the same name, or create a new one if a new name. It will not move a "non-terminal" waypoint, but instead you will end up with both (unless of course you create a "non-terminal" waypoint instead). There probably shouldn't be any need to delete default waypoints.scott s..