What I do, really depends on the type of quest I am doing.
In my more recent quest, Fantastic Dungeons and Where To Find Them for instance, was that I created a whole bunch of example screens which I copy/pasted all throughout the quest for dungeons.
I also made an overworld, and then copies that entire map to a new map. Mainly, cause I intend to make future quests with that same overworld.
After that, I started planning dungeon shapes, keys and item placement for the entire quest. Dungeon shapes were based off of the Straw Hat crew members from One Piece.
That was a very simple quest though.
I have a more ambitious one that I am planning right now, and am working on making several documents for various things.
Thanks to you guys, I used diagrams.net to create a diagram of the main dungeon/pre dungeon progression. It is very basic, and doesn't necessarily cover everything that will happen between dungeons.
My next plan, is to make a document with important information for various parts of the quest. Optional items, upgrades and the like. As well, as defining gimmicks for the various dungeons. Since this quest actually has gimmicks for once.
After that is planned, I will return to making dungeon plans, and build all the dungeons. Then I will make the overworld, and make overworld plans.
The last thing I like to do is polish and write.