Your stuff look really nice.
You will be fine as long as you use floor segments. The characters will not be able to walk across the floor proper if you dont. Entites as walls and other stuff generally work fine. You may need to offset the wall a little if you can find that you can (the player) can walk up to a wall and go thru it a little.
All of our stuff for insomnia is coming are made like this.
So plan your level around the floors and you should not have to many issues. Also by using floor segments instead of entities you can restrict where the enemy can and cannot get to you.