I read the description of their marriage as meaning they are a real team. In such a marriage, sometimes the wife is the strong one, sometimes the husband is, but usually they work together, as equal partners. The marriage comes first, not one person over the other! From what I have read about this era, such a marriage was pretty unusual. (It is pretty unusual now, too, unfortunately.)

Regarding Sophia's winter at Deal, I read the text to mean that she had lodgings somewhere without the Admiral (the Captain, then). He was on a ship in the North Seas, without her. In such a marriage as they had, it must have been extremely difficult for each of them to be without the other -- like having to work without the use of both hands. I've always aspired to such a marriage!