It is a preferred deity, or a deity that has a particular influence on someone's life. For example, Chauntea to a farmer. However, this doesn't mean that someone who prays and worships Chauntea more often/intensely than they do with other deities, thinks that Chauntea is superior or above the others. She simply has more influence on the farmer's life than, say, Umberlee might have.
Also, someone may identify themselves with the cause or ideals of a deity, and choose to dedicate themselves to said deity, but that doesn't mean that the person sees their deity as inherently superior or above the others. And it doesn't mean that they won't pray to other gods, if needed.
Yes, I always thought that it would make sense for your farmer to make sacrifices to Umberlee if they found themselves having to travel by sea but otherwise not paying too much notice to her.