I don't think we know the end of BCS. Vince Gilligan has said the BCS timeline is pre, present, and post Breaking Bad. I'm pretty sure the show doesn't end with Saul in Omaha.
NOTE: The following contains major Breaking Bad SPOILERS. If you haven't seen the show, you are encouraged to watch before reading further.
I think the opening scene of BCS with Saul at the Cinnabon takes place either while Walt is still hiding in New Hampshire or possibly just before Walt kills all the neo-Nazis and dies on the floor of Todd's meth lab. Saul went into hiding out of fear for his life, Huell was missing and he thought he was next. When Saul finds out Walt is dead along with the neo-Nazis he will no longer fear for his life and will return to Albequerque and deal with whatever legal issues remain. He will also return to provide some assistance to Brock, Andrea's son, for whom he helped pay rent and living expenses. Where it goes from there, who knows? Of course, this is all just speculation, but I don't think we can say with any assurance exactly how or during what timeframe BCS will end.