Tres Pelicanos dive shop (who I dive with and cheerlead for) is located downtown (7 minute walk from the ferry pier) and will provide transportation to and from the marina, predominately by taxi or sometimes with the staff in the shop truck. There are other shops that travel up to the piers downtown and use them for pickups and others will require you to go to the marina by your own means. If you do need to take a taxi it is 90 -100 MXN (100 MXN = 5.37 USD at today’s rate) from downtown to the marina, which in the great scheme of things is pretty cheap. Many of the shops have a physical presence downtown and if not, provided you have made arraignments ahead of time, they will normally meet with you in town the night prior to get you set up. The Cozumel forum has multiple threads on who is ‘the best dive shop’ but the bottom line is unless a dive op has dedicated source of new clients (read: in house hotel or cruise ship affiliated shop) there are so many dive ops in Cozumel that they all are pretty good if not excellent, there is too much competition for a poor outfit to survive.
As to beaches they predominately on the south end of the both the east and west sides and the best method of transportation is either a rental car (about $40 USD a day) or a scooter (about ½ that).