Maybe i could ask you in IRC if i have some questions about the Configuration (NB <-> OA)?
I can't really answer much. I don't use any of NetBeans functions apart from auto complete. I just created a NetBeans C/C++ project from existing source and told there my make file was.
I use a script for compiling and running (I don't use NetBeans for that):
make && cd build/release-linux-x86_64/baseq3 && rm vm/vm.d && zip -r /path/to/openarena/modname/modname.pk3 vm && /path/to/openarena/openarena.x86_64 +set fs_game modname +set debug 1 +set sv_pure 0
My source and make files are stripped of engine code (well a lot of it at least, see the Open Arena Expanded source).
Engine changes are usually small and I apply them with gedit.