Im new to FS2004 and AFCAD2 and I have a question, where do you put the AFCAD files for the default airports? Do they go in the same folder where I put my addon scenery?

As stated in the documentation downloaded with AFCAD211, the modified default airport's AFCAD files go into the ..ADDON SCENERYScenery folder. Since the ADDON SCENERY folder has a higher priority in the Scenery Library list, those files replace the lower priority files. If you moved the ADDON SCENERY folder below the other folders, they would not work and the default scenery files would have priority.The default scenery files are not changed in any way. They still exists in the various ..Scenery subfolders.W. Sieffert