Thank you a ton, your advice worked perfectly for Sigil. I actually am interested in having individual launcher files for Brutal Doom for all of the Doom versions just because I like the simplicity of being able to select each game version separately, even if it is more work. But it isn't working like Sigil did. I created another folder under the doom folder called "brutaldoom," just like with Sigil, then edited the emulators.cfg file with the addition of an emulator called brutaldoom. This new entry had /addon/* changed to brutaldoom/*, the same as I did with Sigil.
I placed the doom wad in that folder, and the brutal doom .pk3 file. I set up a "Brutal Ultimate Doom" launcher directing the location of the doom.wad file in the doom/brutaldoom folder. It launches it perfectly fine when I set "brutaldoom" as the default rom launcher, but for my launcher for the normal Ultimate Doom it will then be set to use the brutaldoom launcher as the default rom emulator as well. If I change the normal ultimate doom launcher back to lzdoom to play vanilla doom, the default emulator for the brutal doom launcher will then automatically be changed to lzdoom as well. So changing the emulator for one ultimate doom launcher changes it for the other, whether its brutal doom or vanilla. I assumed that was because I used the doom.wad file in the brutaldoom folder without changing the name, so what happened to one "doom.wad" changes it for the other because they have the same name, despite being in different folders.
So I tried changing the name of the doom.wad file to brutaldoom.wad in the brutaldoom folder, and kept the original vanilla ultimate doom in the doom folder unchanged, but then it won't even launch the brutal doom version. So it seems to have to keep the original wad name. Since what I did what worked for Sigil I'm lost as to what it is making the two doom.wad files, in different folders, linked. You know so much about how it works, is it obvious where I went wrong? I feel like it must be something small that I just keep missing.