Where will you be staying? Everything is aligned along the west coast looking across to the lights of Playa Del Carmen on the mainland. The town center is where the activity is. Just to the north of the town is the airport. North of that are condos and hotels. If you are up there everything is a 5 minute taxi ride or 20-60 minute walk to town along the coast road. There is a sidewalk and even a bike lane for most of this.
About 2 miles south of the town is a cruise port. This is a fake town designed to efficiently transfer money from cruise tourists back to the cruise companies, a handful of international corporations and the Mexican government. A few cents on every dollar even finds its way into the local economy. There are also cruise ship piers in the main town, which means you have to put up with a few blocks of touts and souvenir stalls if you walk along the waterfront road.
South of the cruise piers is the port from which the dive boats leave. More on this later. Even further south are the larger resorts. The most commonly dived reefs are off this southern part of the island.
Most of the independent business including dive shops and restaurants, along with the main grocery stores are in town. Unless you are in an all inclusive or like to nest in your hotel, you will be spending a lot of time and money in taxis if you are staying elsewhere.
The next question is where you meet your dive boat. It's unlikely anyone will pick you up at the northern hotels unless you are chartering an entire boat and are willing to pay for that service. The main exception is Aldora Divers will pick up their divers staying at Villa Aldora. They may pick you up as well, you would need to work it out in advance.
Some ops will pick you up in town, either at your waterfront hotel or one of the small town piers. If you are staying in town and your op won't get you, then you'll need to taxi to the port. Again some ops will arrange the taxis, others leave it to you.
Almost all ops will pick you up at your hotel dock if you are staying south of the port since they are heading that way anyway. But, as always, get it confirmed in writing before you put the money down on a multi-day booking.
Finally, all the larger resorts have a house dive operator. This is the most convenient way to go, especially if you want to do more than the standard two dives per day. But the quality of the ops varies. Search through this forum or ask if you have a question about a specific op.
I've done three trips to Coz. The first time at a southern resort using the house op, the second at a condo on the water in town where we were picked up by an independent op (Pelagic Adventures), and the third staying north of town and diving with Aldora. I wasn't at Villa Aldora, but was nearby and was able to be picked up there when they had diving guests. The other days and for the one night dive I did I walked to town and was picked up there.
The in-town option was my favorite by far. But the next time I go, I'm going to want to combine some shore diving in addition to the morning boat trip which means I'll probably stay at Villa Aldora or one of the few southern hotels that offers it.