Hi @neishy ,
I’d probably make it something like:

The left one is for better seeing what is happening, in the middle one the ‘hole’ is filled with that Face. This way the wall has thickness, which is good.
You can fill the bottom as well if you want, but don’t worry about making it non-manifold, if you’re not going to 3d print it, use Booleans or use a Subsurface Scattering on the walls or floor.