Both my wife and I have Coast Guard master license's. However we share duties on the boat. Docking, she is at the helm and I am handling dock lines. Anchoring, she is at the helm and I am handling the anchor. On long cruises we take watches. When it comes to navigation, we both have equal in put. We have seem to fallen in to a routine which works well for us.
The only hard and fast rule we have is I stay out of her galley and she's stays out of my tool box!