It was never intended for WDC to ever edit games other than Wolfenstein 3D and games that use its engine. Nitemare 3D map editing was patched into the editor, but the process isn't very user-friendly (I admit it myself).
Since WDC can only edit Wolfenstein 3D's GAMEMAPS style map files, you much first create a Wolfenstein 3D-based project. Then go to Import/Export -> Import Map, select "Nitemare 3D MAP Files" in the file type drop down, find the Nitemare 3D MAP file you want to edit (MAP.1, MAP.2, or MAP.3), and hit OK.
Now go back to File -> Project Information and click the "..." button on the "Map Data File" line. Select the Nitemare3D-MAPS*.wmc file that matches the MAP file you just imported, ie: Nitemare3D-MAPS1.wmc for MAP.1. It's very important that you do not change any of the map symbols for these file types because the symbol names contain data in them that also gets translated into the MAP file.
Make your changes to the maps. When you're done, go to Map Tools -> Export Multiple Maps and click the right arrow to move your maps from the left to the right side (MAP.1 has 11 maps, MAP.2 and .3 have 10). This still will be easier if you remove all of the non-Nitemare 3D maps from inside the editor. Click OK, set your file name and save. Be sure to use the same file name as your imported!
Play the game and try our your new levels!
I believe the Nitemare 3D can allow for any number of maps, but I'm not sure.