Basically you still drew in 2d but you could overlap rooms with other lines that wouldn't intersect with any already existing lines, and that would configure 'a room above/below the current room'. Then you had to slope the floor until it actually connected with the newer room.
It was pretty strange but yeah, some people built insanely detailed things with Duke3D :-)
Elaborating a bit -- the Build engine had a feature called "sector effectors" that, when triggered, would teleport the player to a completely different sector in the map. The transition was seamless and permitted interesting effects like the illusion of having stacked floors.
The designers used this feature to most profound effect in the level Lunatic Fringe. In order to complete a full circuit of the central ring room, the player had to move through a 720-degree circle to return to the entrance. It was _extremely_ confusing playing that level for the first time.
https://dukenukem.fandom.com/wiki/Lunatic_Fringe
Fabian Sanglard wrote an excellent series about the engine here: https://fabiensanglard.net/duke3d/