Hokay, as I have my SMC in my Card Reader at the moment, and I'm playing a lot of doom at the moment, let me give you a quick run down...
The Root of the SMC has these directories on it
<DIR> GAME
<DIR> MP3
<DIR> GPSYS
<DIR> GPMM
<DIR> GPETC
The two we are interested in at the moment are GPMM and GAME
OK, in the GPMM directory you need to put:
GPdoom.fxe (That's all)...
int the GAME directory you need to create a DOOM directory:
<DIR> doom
Then in the DOOM directory I have:
<DIR> DOOM2
11,159,840 DOOM.WAD
163,840 DOOMSAV0.D
84 DOOM.OPT
<DIR> DOOM
<DIR> TWILIGHT
15,218,428 DOOM2.WAD
The important file here is the DOOM.WAD file. This can be found either on the internet (the demo version from ID.com) or from an original CD of the PC version.
You just copy that one file into the DOOM directory. The other directories are created by GPDOOM (I think).. But just to be complete here are the contents of those dirs:
DOOM2:
60,589 DOOMSAV0.DSG (I guess from when I played DOOM2 briefly)
DOOM:
70,985 DOOMSAV0.DSG
70,185 DOOMSAV1.DSG
67,989 DOOMSAV2.DSG
55,433 DOOMSAV3.DSG
47,253 DOOMSAV4.DSG
(save files from my ongoing attempt to complete DOOM once and for all!)
and there's nothing in the TWILIGHT directory (left over from when I tried one of the other WADs (or mods if you'd rather think of it that way)).
When people talk about additional WADs they are talking about "homebrew" versions of DOOM where others have used one of the editting tools for DOOM to create extra levels - or even completely new games - e.g. a version of Goldeneye, a Western style FPS, even a version styled after final fantasy graphics... there are a load of them over at Drumaster's site (If I remember correctly).
Some you need the original DOOM2 WAD to play, some you don't.
Hope this helps
Argon0