Welcome aboard, Haley! I just sailed on the Disney Magic last month and was able to enjoy the beautiful waters of the Western Caribbean while relaxing at Playa Mia where the Beach Break adventure takes guests.
There are most likely two departures for the submarine, around 8:45 and around 12:45. Since the
Beach Break will leave around 8:45 or 9 as well most likely, they will overlap. Also, even if times did seem to work out, there is not guarantee that your first adventure would end at exactly the time listed, meaning you could miss the second one. Unless you have two very short Port Adventures with departure times quite far apart, I wouldn't recommend trying both. You would be too nervous about missing the second one to really enjoy the first.
I have done the submarine trip in Cozumel as well, and though it was interesting, I really enjoyed the beautiful Playa Mia beach and would love to take that Port Adventure again. If you are interested in doing both the Beach Break and another adventure, check out the
Cozumel Ruins and Beach Tour which first takes you to the Mayan ruins, then around the entire island of Cozumel, with gorgeous views throughout, ending at Playa Mia for the same beach adventure (though the kids' water park area is not included in this combo tour, only the beach and water activities). My five year old son learned a lot about the ruins, and then we got to cool off in the ocean afterwards! I loved that we not only got some beach time, but a history lesson as well.
There are a few other Beach tour combo adventures you could check out as well.
Good luck deciding, Haley! Let me know if you have any other questions!