In terms of balance, the game is still being worked on and tested so I can't really help with that unfortunately! Right now I'm still figuring out which upgrades players take, how much health they tend to have as they progress, etc., so I'm sort of guessing at balance until I can do more thorough testing with the complete game.
Writing the regions themselves is fairly straightforward. Figure out how many areas you want the player to encounter as a minimum before they hit the boss room and add 1 to it - that's the minimum number your Boss Room should occupy on the Area table. From there it's just a matter of figuring out which areas you want and what you want to be in them, much like writing an adventure or a dungeon in a more traditional system.
Hope this helps!