If you're talking about your 6.5 day trip, they won't filet on board--Mexican law prohibits it. Most of the premier long range boats now offer a choice between freezing your catch or putting it into "RSW" (Refrigerated Salt Water--salt water freezes at a lower temperature than fresh water, this is so cold as to hold your fish just above where the meat will freeze--generally offered only during the last 5 days of a trip because its better to freeze the fish for longer periods).
If the boat offers RSW, I strongly suggest using it--properly done, the quality is much better than frozen.
In either case, when you reach the dock, your fish will be unloaded into carts--regular carts for frozen, slush filled bins for RSW. It is then pushed to the top of ramp. Frozen is laid out next to cones corresponding to the number each angler used on the trip, RSW goes directly to the processor--you have to choose a processor on board so that they know where to send your fish. You could also take your RSW and/or frozen fish home to process it yourself.
The two biggest processors are 5 Star and Mario, but there is at least one other. I use 5 Star, but Mario also has a very good reputation. If your fish is RSW, you can wait while they process it, if its frozen you must leave it so that it can defrost and be processed. If your fish is frozen, or you choose not to wait, you can either come back to pick up your fish later, or have them ship it to you (extra charge for shipping).
You can instruct the processors how you want it processed (skin on or off, bloodlines in or out, size of chunks). Price last year was $.75 per pound in the round.
I took my fish home from my first 5 day trip, and after that experience swore off it. When I got home, I had enough to do with cleaning myself, my gear, etc. Cutting my fish took time, then chunking it and most especially vacuum sealing and freezing it was a b!tch, and then I had deal with a hundred pounds of fish bones and guts. Unless I have a bad catching trip and not a lot of fish, I have sworn off home processing (some people still do it, but not me).
You can also trade your whole fish for canned. In that case, the fish has to be frozen. The trading ratio varies throughout the year and depends upon the species being traded, but generally expect 6-9# whole fish for a 6 oz can.