With the basics decided upon, you’re now ready to look at specific rooms. Before you start on the specific layout of your ship, there is one more question to ask yourself: What does your species value most? Do they value strength or kindness, beauty or functionality? You have already decided what type of ship you plan to make, and that plays a roll. A battleship wouldn’t have a lot of passenger space, like a cruise ship or colonization ship likely would. No, a battleship would be full of weapons, possibly more weapons than the engine or power supply could ever use at once while a colonization ship would likely have massive cargo rooms and possibly rooms for farm animals. A cruise ship would likely need less cargo space as they are only out for a few days but they would need many more recreation rooms like sports centers, arcades, and casinos. A flagship may merely be the first of a type of ship built but if you plan to create the ship the admiral of a fleet travels the stars in, be sure there is a lot of people and rooms dedicated to communications between the fleet as well as heavy weaponry in war times and maybe little weaponry in peace times. (Depending on the admiral, the ship could be more of a diplomatic ship meant to be pretty than a ship designed to threaten.) A science ship may have a massive science department, a large medical department, medium to large cargo areas, and little recreation as well as a small security department and skeletal crew to run the actual ship.
That leads me to my next question: Is your culture more interested in functionality or beauty/symbolism? If your ship is designed to be functional then everything has a reason and is as small as possible without destroying morale nor the use of the object. If your culture is religious then they may have everything from the blueprints of the fictional ship to the decorations on the walls or rooms designed specifically for symbolism, which you should understand. If your culture is very artsy then you may have everything with smooth lines, meaningful colors, pictures everywhere, and rooms specified for specific arts, or your culture could be into abstract art and seem chaotic to an outsider.
The choice of what your species chooses to value is up to you but keep it in mind as you decide how many, how big, and what rooms are near each other on your schematics.