Depth Issues on Inverted Walls

[Digital-Jedi]

So, I fully acknowledge I might be using this plugin in a way that it wasn't intended. But, here's how I came upon this issue.

I wanted to make an arena like structure with hotels on the interior. So I laid a circular foundation, set some floors and slabs and just removed the top. I also took out a few walls, as I wouldn't be needing them. I noticed the balconies were forming on the outside of the structure, so I used Mesh » Normals » Flip to invert the structure. This seemed to work fine up until I tried to place multiple windows or doors on the interior of the walls. (It also placed balconies on the wrong side if I selected all around the interior all at once using CTRL. If I, instead, make the selections using CTRL at the halfway point and then go to the end, it places them on the correct side all at once as intended.) Currently, I'm just flattening the to depth 0, but any depth added causes them to extrude in different directions.