Thanks for the feedback on the demo!
Multiple rooms can be in the same area (larger squares) and rooms can cross over the area borders, too. The main purpose of the areas is to determine the locations of monsters and loot (and the dungeon entrance): the areas don't have any impact on the rooms themselves.
Most rooms must follow the dimensions shown, but some "freeform" rooms, such as the cavern and tunnels, have some flexibility.
We'll try to make everything a bit clearer in the full version coming this August.
Thanks again for the comment! :)