Although the obvious assumption would be to say that the ship has two decks (one above and one below the red line on the hull), it actually must have three. Despite some behind-the-scenes CGI showing how the landing leg opens, which shows the ship with only two decks (thanks to the ever-watchful Leandro Pardini for digging out the picture, shown right), the actual episodes disprove this. 1ACV07 shows that the galley is directly below the bridge (accessed by a ladder), and the mess is presumably somewhere through the double doors aft of the galley. If the ship only had two decks, the mess would occupy the same space as the cargo bay, and the galley would be outside the hull entirely!

The position of the 'engine block' powering the thrusters is conjectural, but really, where else could it go? Having said that, the number of rooms inside the ship is increasing like rabbits on Viagra, so a major reshuffle may be in order soon.

Interestingly, the lower fins on the ship are hollow, as seen in 1ACV03 when Amy is working on something inside one of them. What's in there? Who knows?

Deck 1 is where the crew spends most of its time, as it houses the bridge and (presumably) all of the crew quarters. Quite a few educated guesses can be made about the internal layout from the exterior of the ship, such as the location of the cabins. 2ACV12 finally confirmed that the ship has a central corridor, and also revealed the location of the ship's bathroom!

Leela's cabin was originally on the starboard side of the ship; 2ACV06 seemed to retcon this to the port side by turning the porthole into a mirror next to the door. I moved the laundry and vending room from Deck 2 because I was running out of space down there -- I managed to fit them in up here by moving the airlock forward, since looking at the ship in the show made me realise I'd placed it a bit too far aft on the hull anyway. Of course, I had to move everything around when 2ACV12 revealed the central corridor continues aft of the airlock, but neh.

The computer's 'brain room' wasn't placed anywhere specific in the episode, but I put it at the back of Deck 1 because it seemed to have a lower ceiling than other parts of the ship, so would squeeze into the restricted space under the main fin, and also because I couldn't figure out anywhere else for it to go!

Rooms

Bridge (1ACV01)

Bathroom (2ACV12)

Leela's Cabin (1ACV04, 2ACV06)

Fry and Bender's Cabin (2ACV12)

Professor Farnsworth's Cabin

Hermes's Cabin

Dr Zoidberg's Cabin

Amy's Cabin

Starboard Airlock (1ACV09)

Turret Access

Laundry (2ACV02)
Vending Room (2ACV05)
Emergency Supply Room (2ACV06)

Brain Room (4ACV03)

The layout of Deck 2 is largely based on 2ACV06, where Bender is actually seen with a plan of the ship! Although it's not specified which deck the plans show, certain things can be deduced. It can't be Deck 1, because we know the bridge is at the front and there's a narrow corridor directly aft of it. It can't be Deck 3, because we know that the cargo bay runs the full width of the ship. That just leaves Deck 2...

Because the galley is directly below the bridge (1ACV07), it must be on this deck, and it makes sense for the mess to be nearby. Zoidberg's medbay was introduced in 2ACV05; it looks to be quite a large room, but without any portholes, so Deck 2 is the most likely place for it. Aside from the 'magic hatch' in 1ACV04 not much else has been seen of Deck 2. (I've put the hatch in here because it can -- just -- fit onto this deck.)

At the start of 2ACV02, Fry and Bender are playing chess in a large room which I haven't managed to identify yet. It's most likely the large room behind the galley, so I've labelled it thus until I get more info!

Rooms

Galley (1ACV07)

Mess (1ACV07)

Emergency Hatch (1ACV04)

Medbay (2ACV05)

Deck 3 houses the cargo bay, the engine room and not much else -- and for all I know, I might be wrong about the engine room. As for the undoubtedly fantastic engineering that allows the retractable front landing leg to connect up to the airlock... did you seriously expect me to attempt to draw it?

The extra corridor behind the chamber housing the landing legs was added after 2ACV06, where it was shown that there was a second large roller door visible beyond the cargo bay, and the engine room only has a normal door. Because Fry and Bender both used the rear door to enter the bay, I've assumed that there's another way up to Deck 2 somewhere between the cargo bay and the engine room. Either that, or Fry and Bender sleep behind the containment chambers!

Rooms

Forward Landing Leg

Rear Landing Legs

Main Airlock (1ACV08)

Cargo Bay (1ACV02)

Engine Room (1ACV04)

Dark Matter Containment Chamber(s) (1ACV04, 2ACV02)