1. It is OK to rotate either the front atom or the rear atom, but offhand flipping does not sound correct. I would have to see what you mean, however, before I would conclude that flipping was what was being done.
2. It is typical at the level of sophomore organic chemistry to show Newman projections at 60° increments.
3. Add up the steric energies for each interaction that you find. Let's see your work.
4. In my opinion a wedges-and-dashes representation is meant to indicate configuration, not necessarily the lowest energy conformation. You will have to find the lowest energy conformation yourself.
5. I am not 100% certain what you mean by flipping. However as long as one's representation is accurate, I don't see a problem with, for example, choosing carbon-2 as the front carbon versus choosing carbon-3.