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How do you decide what sort of challenges to present in front of the player where? Is it sort of like, stream of consciousness placement then refinement based on how it feels when you actually play?

More or less, yeah.  I'm not heavily methodical about it.  I usually (not always) have one or two ideas for navigational or logic challenges before I start drawing.  I may have one that spans the whole level or a few smaller localized ones, or both.  I'm not making a puzzle game, so these aren't super complex, I just like (as both a player and a designer) having something to think about other than filling in map squares.  I think it makes the dungeon more fun.  Monsters I just put wherever I feel like obstructing the player, or often guarding the more valuable items.  And sometimes I just feel like being a jerk.

The layout of the map is pretty much whatever comes to mind.  I take kind of a "fun house" approach.  The levels have a theme and the layout and flavor text reflect that theme, so it's not totally random, but it is a dungeon.  It should be a little bit crazy.  I do aim to include multiple connecting paths most of the time, since long corridors with no side paths aren't much fun.

Outside of actual challenges, I just try to fill in as much flavor text as I can think of, so that the dungeon has a bit more texture to it than just a plain series of corridors.  This is easier for some levels than for others.

When playtesting I will often shift around geometry, encounters, loot, etc. to tweak the flow of the level or fill in areas that feel too empty.

For my action games, I guess the overall approach is similar, just with less forward planning.  The levels for those games haven't been nearly as dense, so drawing them out on paper hasn't been necessary.  If I were making a Metroidvania or something, though, it might be beneficial.

Btw, def gonna check out your MM0 game, i love a good dungeon crawler like that, wish there was more of it being made out there lol

Cool!  If you do, let me know what you think.  I am always interested in feedback from dungeon crawl fans.  It's pretty basic (it was made for a jam, after all) but I think it turned out well for a first try.  I'm working to improve on the next one.