This is the way I do it:
I duplicate my q3 installation. One clean, one "dirty". The "clean" one has only the vm, the pak3.99a, and that's about it. You should be able to fire up q3ctf1 and play it.
In the duplicate directory, in gtkradiant, I set up the fs_game as wfadev, and do everything from there. The only thing you need in that directory is what comes with 3.99a really. You can extract what you want, but nothing is really needed to be extracted except what you want to edit (for a merge back into the "clean", or formal, wfa)
This means putting the surfaceparms.txt, the entities.def file, everything in the wfadev/scripts directory.
This way, once you package your map, you can put it in your "clean" wfa directory and see if there's any problems.