They're split between the officers and the crew pretty much like the navy and they all serve under a captain but you're still a civilian worker so you keep your basic rights plus any rights given to you in your contract with the union/company you're working for. There are three main departments between the Engine, Deck, and Steward that you can work in and you work under a chain of command that goes from the captain down.
The crew though this tends to change when dealing with Navy and Military Sealift Command ships. Because those tend to have positions for people with a higher technical expertise and focus kind of like electronic/computer techs and shit like that I'm pretty sure. They've even got medical doctors/nurses on them called MDRs.
My last ship was a Navy ship ran by a shipping company called Maersk that ran through the yellow sea pulling a radar array behind it. I worked with navy personnel but by no means did I work for them or have to do anything that they wanted me to. Now the captain was their bitch, and if he were to tell me to do something that their masterchief or whatever ordered I'd have to comply to keep my job. But I could also tell him to kiss my ass if I felt that I needed to. Which is what I like about it so much.
But they could stick me in a closet and call it a brig till we got back to shore if my refusal to do something or some shit like that endangered the ship's mission or crew. But legally thats all they could do until we got to shore where they can fire me but I still wouldn't have to do a damn thing they told me to and I like being able to have that freedom just incase I need to use it one day.
There are also a few red cross ships in the fleet that are under MSC command and go to third world countries/disaster areas to give support. You can work on all kinds of science study vessels but the really cool shit like that and ships that go up into the arctic/antarctic to do studies. Buts its kind of hard to land one of those jobs unless you know someone or get lucky because they're kind of scarce from what I understand.