WDC is at its heart solely a Wolfenstein 3D editor, but I've managed to patch in the ability to edit Rise of the Triad: Dark War maps using the same technique that was used for Nitemare 3D maps.  Again, this process isn't very user-friendly.

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, find the RTL or RTC file you want to import and hit OK.  This will import all 100 maps from the file, which will require you to recompile the GAMEMAPS file using the new settings for Rise of the Triad.

Now go back to File -> Project Information and click the "..." button on the "Map Data File" line. Select the ROTT.wmc 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.  Click OK, set your file name, and save.

Play the game and try out your new levels!