They give pretty good instructions on the web site.
http://www.afadoomer.com/wolf3d/howto.html

Its pretty awesome too as it combines EVERYTHING into the same menu (if you use the 'consolidated' launcher). So when you start a new game you will see a list of every Wolfenstein 3D game. The only Wolfenstein 3D games not part of the port are the console versions (Mac, SNES & Jag versions). That said there is an option in the mod to enable Jaguar weapon sprites which look a lot better, though perhaps not as WWII as the classic sprites. The MP40 has been transformed into some sort of M16 rifle for example.

You can see the start menu in this video. Also the user is using the Jag sprites.
https://www.youtube.com/watch?v=a_KTxmg6ENA

Yah, following the instructions I just get an error message when I try to use the consolidated .bat . "GAMEINFO line 1 Unexpected character o(accent) ASCII-11".

Do I need to drag files from SOD and WOLF3D into the zDoom folder?

Apparently the version of ZDoom that site links to is outdated. Grab the very top file from this site.

zdoom-2.8pre-1779-gbeb2a4f.7z Sep 27 2015 20:11:50

http://devbuilds.drdteam.org/zdoom/

I just tested it myself and it works fine.

EDIT: You may also want the latest version of GZDoom. Some Doom mods require it and it just looks a bit smoother... though some prefer the more pixelated look of standard ZDoom. You can extract both ZDoom & GZDoom in the same folder.

http://forum.drdteam.org/viewtopic.php?f=23&t=6482&sid=dafc1c78333543dbccc97da7e53bafeb

Tested the latest version and it seems to be compatible. Download "gzdoom-bin-2-0-05.zip" in the attachments section of the first post.

<3

Works perfectly with no effort. Thanks a lot for the help!

Beautiful, I might have to pause my Resident Evil playthrough to finally play Spear of Destiny again.

Have you tried using ECWolf? It is a source port for Wolfenstein 3D, so doesn't play like ZDoom with the textures floors and ceilings and levels are indeed flat as it uses the original Wolf data files, but it does have the option for an automap (at least, it does in the nightly builds, anyway, can't remember how far the latest non-beta release got).

The latest ECWolf release runs great. The same guy who created it also worked on a port of Super 3D Noah's Ark (same engine) for Steam and worked on the ZDoom project. I bought a copy of Super 3D Noah's Ark partly because a portion of the sale goes to him and I feel he deserves it after all the awesome sourceports he has worked on over the years.

http://maniacsvault.net/ecwolf/

While I've been pushing the ZDoom Wolfenstein ports and TCs there is absolutely nothing wrong with ECWolf and it provides the closest most pure version of Wolfenstein 3D, besides DOSBox of course. I personally prefer a lot of the extra Doom features in the ports.

Plus ECWolf supports mods. I've played the following Wolfenstein mods using ECWolf (though the mods have to be ECWolf compatible, the old Wolf3D mods won't work until they are fixed for ECWolf):

Assassinate Hitler
ECWolf Tech Demo
ECWolf Tech Demo - Expansion Pack: Return to Totenhaus
Astrostein: Spifferaneous Edition (that I found a few days ago)

Looks like I might try ECWOLF then. I only finished one level in ZDoom so no big deal.

Thanks for the tips guys! I haven't played SOD in over 15 years (?).

You can just copy the ECWolf files into each of those respective folders and run it.

You kids today are soft.

..

Oh boy. You're not kidding. I am playing in GZDoom, and just started Mission Pack 2. I find no gold key for the gold key door on Level 1, pushwalls that end up blocking doors and treasure, then I get to Level 2 and check the map...to see 3 enemies strolling off the map edge into infinity! TC was too faithful to the original :D

Well, yes if you want to have three instances of ECWolf, but it's not very efficient, and it is three additional copies to then maintain with the beta builds (I always use the latest build available, so only having one to extract works nicely).