With FQM 2 (Deluxe), it not only makes sense, it is necessary. You can not make a map with FQM 2 and then load it in any other mod or the normal game. You must use the data files in FQM 2 to play with the map.
Fyron, I'll bet that is all in the Readme somewhere. You may be getting an idea why I did not do very well in school. It was never a lack of trying but it could have been worse.