I've recently become enamored with the Swords of Abandon project at Sword +1. I'm particularly interested in his Ugarit project as I am both a fan of large underworlds and neat maps. EPT was also one of the largest influences on my recent Uz project. While it's obviously more based in real world cultures, EPT was what I was reading when I was working on it, and I almost thought about using it (or Swords of Abandon) as my system for Uz.
The Uz sessions took place in a Barkerian Underworld: I printed out four sheets of 10x10 to 1' graph paper, which would be a tiny bit smaller than one of M. A. R. Barker's underworld levels for EPT. Then I set about mapping. I only got one of the four sheets mapped out completely, but I figured that was enough for what would be at most three sessions.
In reading EPT I discovered something I'd never known before. Barker didn't conceive of "Saturday Night Specials" the way they are explained in B/X and Mentzer. In EPT a Saturday Night Special is not a single chamber but a complex designed for a special and fantastical purpose. The examples he gives are not a well that changes your hair color every time you drink from it or a magic mouth on a stair case. Instead, they are temples, tomb complexes, and the abodes of demons.
This forced me to think about "specials" in a different way. Before filling up the rest of the dungeon, I placed a tomb, a temple complex, and a system of caves filled with degenerates on my graph paper. Then I wondered: should I fill in the intervening space? M A R Barker says that one could either leave it empty, or generate it randomly a la Gygax's various tables. I decided to map it off of feeling, as I usually do. I drew rooms in random positions because I liked the way they looked there, or the way the hallway was shaped. I differentiate this from the random method, but that's more or less what it is.
Still, I could have left it empty, which is essentially the way the 3.5 version of the CSIO (and I presume the original Wraith Overlord) handles it. I see merit in both systems. The empty space version is obviously more "realistic," and strains credibility less. Still, the packed in and randomly stocked extra rooms add a kind of fever dream quality I really like to see in my "underworlds."
I'd probably stick to the method I used if I were to design the rest of the underworld because I think it provides more play opportunities. When I ran Uz for the Hattiesburg group I only stocked the "Saturday Night specials" -- including the empty rooms and minutiae -- and then stocked the random rooms as they went. It seemed to work fine.