In Isla Mujeres, you have to check in at the harbor - that's the only place.
We just got back from there on Thanksgiving. We stayed at Marina Paraiso for a week. I'd contact them, they have an agent on the premises that can help you out. That's probably the best marina on the island, and certainly a good place to "arrive" to. It is also pretty reasonable, and you can't beat the food
at the restaurant. Seriously. It's also hard to beat 5 beers for $80 pesos.
Marina Paraiso Isla Mujeres