I dive at aquarena frequently and have DM'ed there for OW classes on several occasions. The area was closed for a year or so to remove the sunken sub, several buildings, and restore much of the natural feel to the area. It's a very nice place to dive, and I believe they have restarted the science diving class which certifies divers to dive in the springs.
For OW classes you are limited to the training area which has a maximum depth of around 15 feet. It's almost more like a pool setting than open water. I don't believe doing your certification dives there will prepare you well for Cozumel diving. But, that said, I would still recommend doing your dives there before your trip, but plan on hiring a private DM, preferably an instructor, to work with you on your first few dives in Coz. The reason is that you will have some valuable skills practice in the training area at aquarena and more experience when you arrive in Cozumel than you would if you did not do the dives. This should help you to be ready to focus on developing good buoyancy control and dealing with the depth in Coz. You might even consider doing AOW in Cozumel, if you're motivated. This way you could continue to work with an instructor throughout the week in Coz. If you get a good instructor there (I'm sure there are many!) you could learn quite a bit.
OTOH, if the certification dives in aquarena are fairly expensive, and money is tight, you might do better simply extending your vacation a few extra days if you can to do the cert dives and a full week of diving in Cozumel.
Either way you'll have a great time!
