Yes, the "Adama is the Fleet Commander" is the only direct reference to the command structure in the episode. I think this is one case where taking the series as a whole, it becomes easier to infer certain points and the fact that Cain always appears in a warrior's uniform and not the more formal command uniform that Adama always wears, would also serve as a good subliminal indicator of how in the overall scheme of the Colonial Command structure, Cain would place lower than Adama.
The one underlying point regarding Cain's motives that I don't think came out in the episode or the novelization has to do with the matter of why Cain is determined to keep fighting at this point.
Cain is described as the greatest warrior in the Fleet's history. And just think of what Cain has to deal with with the realization that he wasn't there to do anything about the destruction of the Colonies? That fact alone has to weigh heavily on his conscience, because no doubt his own sense of confidence in his ability would make him think that if he had been there, he might have made the difference.
So Cain's determination to keep fighting is best seen not through the too narrow prism of mad egomania, but with the much deeper subtext of guilt that his decision to not return home after the Battle of Molocay may have been the most tragic mistake of his life. Taking out the baseships to try and give Adama and his Fleet his idea of long-term security, is thus at this point the only way he can think of to make up for that, and if he isn't successful in taking them all out and survives, he then would consider it an obligation to keep tying the Cylons down and hopefully buy Adama more long-term security.
Just my take on this very fascinating character.
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