Could be Neegan has different outposts and a main settlement. The outposts could be for his army of thugs who roam the area, killing those seen as a threat and to intimidate other groups who they deem as weaker than them. They forage, dispose of walkers etc. He may also have a more disciplined army who protect the main settlement and keep tabs on the thugs. His main HQ could be a safe haven for those he sees as the elite, i.e, doctors, scientist etc, people he views as most likely to form the basis of a new civilisation.