- don't use hollow
- don't use substract
use the clipper and build all your holes manually. Build your rooms manually.
Every tutorial I ever read always starts with 'make a room' 'make a corridor'. While this is good starting point to explain brush-handling,
it is, in my opinion, not the best way to make your map. I always start with the inside (in detail brushes) and I put walls around it when it's is finished.
Think like this: a hole is not something you make by removing pieces of brushes; a hole is that what remains after you have build all your walls and insides.
Using substract to create holes, will cut your wall in weird ways. It won't be that bad for a cubical hole, but it certainly is for more complex shapes. The obvious example:
On the left side, I substracted a 6-sided brush from the wall, on the right side I constructed a clean hole by hand, with the inside in detail brushes. Note that it is very likely that the left example won't be grid-aligned!
Bottom line: if you can do it cleanly with substract, you're probably better of using the clipper. (Hint: enable the option clipper uses caulk in preferences)
Hollow is evil because it creates overlapping brushes. If you use it, make sure you fix the result properly. (Hint: the thickness of the brushes created from a hollow operation will match the grid size)
Edit:
The clean hole is much easier to edit:
