A couple more "best" practices from my experience mapping and running a megadungeon. For the rest of the series, click here.
Mark the Connections on the Map and the key.
Like it says. On each map, mark where the connections go to with numbers.
For example, you have stairs down on level 6, in room 45.
Unmarked stairs? Bad.
Stairs marked "to level 7"? Mediocre.
Stairs marked "to 7-5" or "to 7, rm 5" where 7-5 is room 5 on level 7? Excellent.
On the map of level 6, you want it to say "to 7-5." On level 7, mark the stairs up "to 6-45."
In the key, Room 7-5 should have a note saying "stairs up to 6-45" and conversely 6-45 should have "stairs down to 7-5."
If you're using a digital key, this will allow a quick "Find" for connections. On a paper key, it'll save you some shuffling. Done right, you won't need to spend time dealing with connections but smoothly go to the new location.
Write Down Small Details on the Map
I know some like to put lots of information on the map, and basically dispense with the key. I find I don't like that, because I always want unlimited room to expand on the detail and I don't want to look in two places. But it's a very good practice to mark small variations (exact widths of tunnels, visual cues in the area, presence of tracks or dampness or dropped lightstones) right on the map. It'll make your life easier both immediately (when the party turns back and doubles back on their own paths and you need to re-describe things) and in the long run (when they return.) This information doesn't need to make it to the key because it's only relevant when you're looking at the map anyway.
You want the map and key to support each other, but not have two sets of overlapping information you have to merge live, or have to keep updating.