Best software & workflow for multi-level (probably isometric) dungeon mapping

[aaronil]

It's been a while since I've had the pleasure of working on a mapping project, and now boy do I have one! And questions!

What is the best software and workflow (e.g. hot-key setups, functionality scripts/add-ons, interaction with other software, layers setups, and so on) for mapping out a dungeon that features verticality and some complex design elements?

My hunch is that due to this dungeon's nature it really needs to be expressed in an isometric view so all the vertical interconnections can be easily grasped.

Here's my initial rough concept map for Krak al-Mazhar, Citadel of the Shadow in the Flame.



More info on the dungeon:

 

Krak al-Mazhar's entrance looks something like this:


It is built into the inner ridge of a caldera like this:


Thus, much of the structure is rock-carved and imbedded inside the caldera ridge, with only a few watchtowers, minarets, and aeries emerging through the rock.

Lying at the heart of a haunted hostile desert, it is the secret hideout of the Brotherhood of True Flame, an evil secret society of flame mages, fire priests, assassins, and their slaves and minions. Roughly 600 human inhabitants occupy Krak al-Mazhar at any given time.

About my skills: I'm conversant with Photoshop and teaching myself Sketchup. Also familiar with a few other programs but they tend to be way more of a time-sink than I'm ready for. I have an aversion to Campaign Cartographer, even though I'm roughly familiar with AutoCAD, mostly because I feel it's inefficient with my time and doesn't give me the results I want. I feel like Photoshop might work if it had a few tweaks (e.g. real-time display of distances/pixels of lines and objects), and I feel like Sketchup might work if it had a few tweaks (e.g. a RPG map isometric cutaway like the old Ravenloft maps, instead of just taking a section).

I've read Jonathan Roberts' tutorial on making an iso map from 2D in Photoshop/Gimp, and that approach has potential.

I'm also eagerly following development on Dungeon Builder, a simple isometric mapping software.