Everything needs to be short named. That means the folders and the wad can't have any spaces in them. If you cna't get it working after that then my guess is you don't have any experience using the command line and that is your real issue and not the program.
(BTW.. Yes it simply patches you existing wd file, it doesn't make a new one.)
I've been fighting with the same issue until I copied the .wad file to a network folder. It worked fine after that. No idea why, but there you go - it can't do it on my NTSC c: drive (my user has full rights) but it can on the network folder (also NTSC file system, but over a SMB drive letter share).