To provision for your bareboat or captained charter, you basically have three options:
1) All In One Shot: Get a cab from the airport, and take the entire crew and your luggage (maybe best you get a van?), and head directly for Loreto, just five minutes to the north. Hit the stores, then head 25 minutes south to Puerto Escondido and your awaiting catamaran.
2) Divide and Conquer: Get two cabs and split your group. One cab heads south to Puerto Escondido with all the luggage, to check in with WCM and get gear settled on the boat. The other cab heads into town to provision and then head for PE.
3) Slow Roll: Get your cab to Puerto Escondido for the entire group, check in with WCM, get settled on the boat, grab some quick necessities from the small market at the marina, and then plan a provisioning run to Loreto in the evening, or early the next day. You can rent a car from Alamo at the marina for as little as $40 for 24 hours (check with the marina office upstairs when you arrive). There is often a cab at the marina each morning, or the office can arrange for one to pick you up. The marina also has a shuttle service, so you can check with the office about a schedule.
The Market at Marina Puerto Escondido is quite well stocked for a small market, and is great for restocking some basics or grabbing something you forgot, but will not likely cut it for a full provisioning run.
There are a number of grocery stores and small markets in Loreto. You will likely be doing most of your provisioning at El Pescador and Ley Express, just five blocks apart from each other on Calle Independencia. These are full-size markets by Mexico standards, but availability and quality of items (in particular produce) will vary weekly and seasonally. Often when one store is short on something, it can be found at the other. Be ready to be flexible, try brands you don’t find in the US, and get creative with your planned recipes. Both accept credit cards, but you will likely want some pesos to tip the baggers.
Most of your alcoholic beverages can be found at these two markets, but the best selection and pricing seems to be at Cactus Liquors, just down the street from El Pescador.
There is also a warehouse-style food and home goods store called Bodega Aurrera, further down Calle Indepenencia from Ley. Fewer produce options here, but quality seems good. Lots of grocery items available in economy/family sizes.
If you need pesos, there are ATMs at the airport, and a Bancomer on the square in downtown Loreto, about a two block walk toward the water (east along the tree-covered pedestrian walk) from El Pescador.