Q: I seem to be having problems with making my floor tiles on ground level, my floor tiles seem to be on roof level, is there an easy way to change this that I am missing?
A: Page 5 of the Editor PDF guide, the Roof button (in the art object toggle panel) should be off (in) for laying floors, on (out) when laying roofs.
Q: What's the best way to fill holes in walls, or better yet, prevent making walls with holes in them?
Two of the wall units are invisible items that will block the hex. The tiles are 620 and 621.
620 = Normal wall (well, normal hidden wall icon_razz)
621 = Shoot Through (that's what the s. t. means), Used like windowed walls.
One shows up on the pipboy map, the other doesn't. If the walls are placed correctly, just put that invisible blocker in the appropriate spots to plug the holes.