I don't know that anything in this post is new, but one of my players asked last session about how I map my megadungeon.
As in, is it digital? Paper? Master copies or copies of copies? Etc.
Here is what I do:
1) Decide on the area size. I pick graph paper size based on that. I use 8 1/2 x 11" or 11 x 17" 8-squares-to-the-inch graph paper.
Probably would have been easier if I'd done hex paper, since I play a hex-based game, but whatever.
2) Draw the map. Next, per lots of posts I've made, I draw the map.
3) Make a bunch of copies. Like, 4-5 copies at least off of the original, which then goes into storage. A copy also goes into storage elsewhere, just in case I have some kind of spill or problem.
4) Stocking Pass. Then I take one of the copies, label it "Stocking Sheet," and do a first-pass stocking. That is, mark special rooms and pre-decided bits (like, "dragon" or "big temple" or "magical spring" or "treasure room.") After that I roll using my stolen from old D&D stocking methods. I mark the numbers I roll directly on the areas I roll for.
5) More detail. On the same copy, I start rolling on my monster and treasure tables. How tough, how rich? This gets scribbled down. ("Fodder, Tough, Many + 10000" or "Boss, single + 0" or "Worthy + 25,000")
6) Numbering. Now, on a new sheet, I go and number the rooms.
And that's it. The numbers get connected to the details scribbled on the "stocking sheet" in the big Felltower.docx file on my computer.
And that's it - we play off of that. Permanent changes get marked on my maps, as do temporary ones. I sometimes go back to the original and make changes there, if I feel it may warrant a re-write of the map as it gets worn. Level 1 and Level 2 maps are badly worn by now, since my players love to tread and re-tread those levels. But generally, it's done at that point.
I really should scan the originals and number ones - and I will, when I get some time with a large enough scanner. In the meantime I'll take some pictures just in case.