The Course of Empire (2003) by Eric Flint and K.D. Wentworth...? It was the first book in the Jao trilogy.
The Goodreads synopsis notes that Earth had been conquered by the Jao twenty years earlier, and that both humans and Jao were now under threat from a third race, the Ekhat:
WOULD THEY DESTROY EARTH IN ORDER TO SAVE IT?
Conquered by the Jao twenty years ago, the Earth is shackled under alien tyranny--and threatened by the even more dangerous Ekhat, who are sending a genocidal extermination fleet to the solar system. Humanity's only chance rests with an unusual pair of allies: a young Jao prince, newly arrived to Terra to assume his duties, and a young human woman brought up amongst the Jao occupiers.
But both are under pressure from the opposing forces--a cruel Jao viceroy on one side, determined to drown all opposition in blood; a reckless human resistance on the other, perfectly prepared to shed it. Added to the mix is the fact that only by adopting some portions of human technology and using human sepoy troops can the haughty Jao hope to defeat the oncoming Ekhat attack--and then only by fighting the battle within the Sun itself.
The Goodreads synopsis for the second book, The Crucible of Empire (2010), notes that the humans and Jao joined forces to defeat the Ekhat, and that their relationship was forever altered as a result of that alliance:
When humans and their Jao overlords joined forces in a desperate battle to save the Earth from the malevolent race called the Ekhat, the relationship between the two species was changed forever. Two years later, humans and Jao are learning to work together in an uneasy alliance.
Searching the Google Books preview for the first book brings up multiple hits for the terms "seal", "clan", and "submarine", including the follow sentence about Earth's fleet of submarines being refitted:
Cables snaked across the concrete floor and up into the sleek ships as the race to refit Earth's fleet of submarines went on.