The first thing I do is slap together geomophs in a pattern that roughly fills up a 6 to 1" sheet of graph paper. This usually takes about 20 geomorphs laid out in a rectangle (5x4). I make sure to get them from varied sources, but I prefer the ones that make their geomorphs available in pdf form. If possible I prefer to do things by hand with pencil and paper and cut out geomorphs as opposed to computers. As I copy them, I fix dead ends, cap the ends, and otherwise change the layout to make more sense as a cohesive level.
Here is a now outdated map of the second level. I made this one using MS Paint, and it fits a full 8 to 1" piece of graph paper, and therefore is considerably smaller than my current dungeon plans.
click to embiggen
Then I set about stocking the thing. I estimate that a dungeon of that size is roughly 100 rooms (it's sometimes more and sometimes less) and use the LL percentages for dungeon stocking to figure out what the rooms should contain. I tend to fill in the "specials" first, but if I don't have any in mind I usually start with groups of monsters.
To do this, I use the "Dungeon Random Monster Level Determination Matrix" found on page 174 of the DMG. I then roll on the appropriate chart in the Fiend Folio to determine what monster inhabits a room. I reroll any results make since for the individual level until I get one that does make some semblance of sense. I use the Fiend Folio charts to determine the number of monsters, raising the die number as appropriate for deeper levels.
I take the results down in short form on a piece of paper. Then I go about placing traps of various sorts and the treasures associated with otherwise empty rooms. After I've come up with all the possible monsters, treasures, traps, etc. I place them in whatever rooms on my map seem appropriate.
Last, I come up with a random encounter chart for the dungeon level. To do this I take the Random Monster Level Matrix and associated 6 different monsters with each result. So if a random encounter shows up, you roll 1d20 to determine its level and then 1d6 to determine the individual monster. Occasionally I'll associate an especially unique monster with a random encounter instead of the an individual room. If the monster is slain, its result is replaced with a more common dungeon foe.
So that's more or less how I stock. I occasionally use the RC or the Mentzer Red Box as well, though I tend to stick the DMG, FF, and LL.