Emergancy Repair Shop

Another specialty shop onboard many naval ships is an emergency repair shop. On US military ships, it’s called the DC shop or Damage Control shop. They deal with things like making sure the fire main is working properly and all the fire hoses are properly repaired to fight any fires on ship. They also keep track of things like all the repair lockers (the central areas to hold things to repair any problems like firefighting gear, flooding cleanup, pipe patching gear, hull rupture repair equipment, and shores to hold up sagging bulkheads(walls) and overheads(ceilings). There are so many frames on a ship to each repair locker with an extra locker near the main machinery spaces) and gas masks in case of chemical attacks. These are also the people in charge of the drills that are run weekly to prepare for the possibility of an emergency. Out on the high seas a ship can be hours away from any other ship. If disaster strikes the only help available is the crew so they need to be prepared for anything at any time.

Electrician's Shop

The electrician’s shop is one of many specialty workshops designed to make repair easier. If you have a problem, all you need to do is determine what type of problem you have and send a request down to the shop that deals with that type of problem. On naval ships that is a little more complicated because there are a number of specialized electrician shops (one works on phone cords, one works on computer wires, another works on engineering wires, and others work on other wires and cords as well as the power boxes). However, we are talking about a fictional ship. There is no need to create so much confusion; you may just want to have a few divisions in one shop or one helpline for all electrical problems.

Waste Management

Waste Management on a naval ship is called CHT (Collection, Holding, and Transfer). There are three types of disposables on a ship: waste, soil, and solids. Solids are all the things you would throw in your trash such as food waste, paper, plastic, metals, and all that stuff. That is sorted and put in a special room. The paper stuff gets compressed down and all the solid stuff waits until the next port where it gets passed down a chain of crewmembers to the proper dumpster on the pier. Waste is from things like showers and sinks. That is usually recycled back into the ocean unless a country specifically asks that ships not do that near their land, in which case it is held until it can get pumped into a sewer system in port or the ship is clear of their area. Soil is what comes from toilets when flushed and that goes into tanks. Occasionally those tanks are slowly emptied into the ocean water to become part of that ecosystem in a small percentage but often the soil is kept in the tanks until it can be released into sewers at ports.
It seems wasteful to just dump trash in space as the ship goes by. Not only is it difficult to determine where the trash will land at high speeds (if you decide to do it this way I’d recommend waiting until the speed is slowed to discharge) but there is no way for space to recycle the trash. If solids accidently fell over the edge of the ship in water (as happens in many private small ships) the water will eventually reclaim the materials and reuse them. (True, that often takes years or decades.) In space there is nothing to corrode materials so they will merely float in place for centuries and beyond (by modern understanding on space). As to waste, the ocean merely adds it to the salt water there, what little dirt or sweat there is gets strongly diluted in the ocean to be harmless to the environment. If soil gets in the ocean, it also gets diluted instantly to harmlessness, unless it is near land in third world countries that have enough of that type of soil in the water to not allow foreigners to swim in their beaches. In space you will likely need some sort or recycling system, which is why I highly recommend a replicator system for long voyages. As for soil and waste, a water purification system would work well. All you need to decide about your fictional ship is if the dirty stuff separated from the water is reused somehow, burned to ash to store easier, or merely compressed and disposed of by special waste ships that transport it to waste planets or shuttled down to planets to decompose, possibly changing the ecosystem in the process.
Another type of waste you will need to keep in mind concerns the air. Humans need oxygen to breathe safely but we breathe out carbon dioxide. Even as big as any ship is, it will need to create more oxygen to keep everyone healthy. One way to do that is through a purifying system using water, but it could also be done electronically on ships if the right technology exists. How will you deal with all the wastes on your ship?

The Brain of Engineering

The log room is the brain of the Engineering Department. This is where all the officers meet each day to discuss any problems or training for that day. This is also where a few important log books are kept, such as the one that says each speed increase or decrease, when it was ordered, and why. Before you start planning this you should decide if everyone will be standing to discuss things with the department head or how many will be sitting? What is the hierarchy among the officers and enlisted at that daily meeting? How any will be present each morning? Also, how many logs are kept there and how are they maintained? Are they computerized, pure paper, or something in between?

The Engine Room

The engine room is the main space for the ship’s propulsion power. Here is where you have to decide how big the propulsion system is, how many people are needed to be in the space at all times or how often they have to check on the machinery in the space. (I would recommend at least once a day since this is such a necessary system and computer readings aren’t always accurate. Having someone manually check the gauges daily or hourly although a computer system likely monitors the system may seem redundant but catching a problem or discrepancy fast can mean the difference between a smooth or hours of blackout or not being able to move while they try to figure out why the system won’t operate. Besides, almost everything the military does concerning maintenance is redundant. That’s why things operate so long in the military.)
Also in this room is electrical power system on the ship and you need to decide the specifics on this system as well. Many ships have all the parts of each system in one huge room but with the right machinery you can put it in many rooms or two rooms. On ships with the systems in two rooms, the second room is often called the fire room. Another thing to think about when dealing with power systems is that they give off a lot of heat. If you want to use that heat somehow, such as geothermal energy, it’s helpful but you will likely need a cooling system of some sort to protect the nearby metal or machinery.

Main Engineering Room

The main room for Engineering Department on a Navy ship is called Damage Control Central, or DCC, and in many science fiction shows as Main Engineering. It is basically a room that can monitor every major system Engineering is in charge of from one place. In most of the Star Trek shows Main Engineering as the room where the main part of the propulsion system was, the warp engine. However, in Navy ships DCC is merely a room with a desk, a few chairs, and lots of panels with lights showing alarms and random noises as smaller alarms go off as scheduled or to denote things that are being worked on but that met overload mode. It is less than a minute away from the two main machine rooms: engine room and fire room.

Departments on a Ship

Each US Navy ship is divided into at least seven departments: Engineering, Operations, Deck, Administration, Medical, Communications, and Supply Departments. Each department has its own chain of command based on rank and specific knowledge. (You go to this person to figure out a problem in one system but another person or division to work on another system.) Each department helps each other and the culture on a ship is often one where the right hand washes the left, so to say. When it comes to covering up problems, not so much but favoritism/friendships and favors are a huge part of ship life as it tends to get things done faster.
Engineering Department is where all the engine and power plant would get maintained on your fictional starship as well as all the piping and fuel needs on ship. On Navy ships they also take care of the balance of a ship underway and are the most highly trained to fix any damage created by hitting something or a battle, or even common wear and tear. It’s called Damage Control and their drills are another major part of ship life.
Operations Department runs the ship. They steer the ship and keep an eye on where everything else nearby (other ships, land, reefs, planes, all that) is so they don’t hit anything. Operations is also the department in control of weapons of attack or defense onboard the ship.
Deck Department is the miscellaneous area of the ship. Their main job seems to be making sure the ship always looks its best and to stand look out for what computers may miss.
Administration is the department in charge or all the paperwork involved in updating records, dealing with schooling or college, and all the paperwork involved in weekly ship and system maintenances. You will need to decide how such paperwork is submitted and recorded for inspections on ship so you may want to keep the question at the back of your brain to think about.
Medical handles everything from simple colds to emergency surgery or stitches as well as the basics of specialized medicine like the typical female issues, references for outside surgery, dental issues and exams, vaccinations, and possibly things like pregnancies or life threatening illnesses, depending on how long you plan to be gone.
Communications mainly handles the traffic between ships of the fleet and the wires on the ship as well as many of the antennas aboard.
The job of the Supply Department is to make sure everyone is fed, has all the supplies they need, and has enough sugar, caffeine, and microwavable dinners to be in a mild mood. They run the vending machines, barbershop, post office, the laundry services for the officers, and are well trained for the security of the ship using handheld weapons.