Spawn location can be in either of the clan halls, can be setup via console in desired hall.
You should build halls in order, no way to avoid this. Personally I decided to build each hall on its own floor (more costly in regards to Forma, more logical overall): smallest hall on the first floor with array of reactors, next one - upstairs with a place for barracks, another one, on third floor - R&D department with labs, etc.
Yes, there is, there's invert button when you're building it. Blue color means it goes down.
Don't know about 4th question, honestly, guess they are deleted