This is just a little insight on which decks I decided to put on the page and why I did, and what their function on the actual Deepwater is. Also, billions of thanks to AMJ for the screencaps of the different parts of the ship.
I picked the Cryo Chamber for the first deck simply because that was where everything began. It was the setting of the first scene in Awakening, it was where the crew were "born" and the first step of the mission (that is, after loading the gene bank and leaving the Solar System) began there.
This is also where the crew first learned of their mission, in Lullaby; the site of the first prex; and the place where the Pandora Virus had been kept.
The Cryo Chamber, like other parts of the ship, is multi-functional. As well as having the six cryo-cloning capsules that the crew awoke from, it has a food synthesizer, a shower, and an analysis table. It also has most of the ship's medical equipment and is used as the ship's medical bay, so Lise spends most of her time there.
Well, I personally have no idea what its function on the real ship is--we didn't even know it existed until we found the symbol for it in the DWB signage file. Then, in the reruns, I saw the Bio Room symbol--in the Cryo Chamber. So I just did away with accuracy for the Bio Room. I just made it a completely other deck because we don't know what's on Deck 2 either. As for function, I'd think that this is somehow related to the Gene bank, but like I said, we never found out.
This section contains bios, it's called the Bio Room, and I figured, why do unneccessary thinking? =D
The Command Deck is the 'brain' of the ship (besides Gen)--everythng is centred up here, and there are interfaces to pretty much all the systems on the ship here. It's the Bridge for the Deepwater, and it isn't carpeted, it doesn't have padded seats, nor is there a "captain's chair" for someone to step into. Yeah, this show really is anti-trek. =D
Engineering: This is Reb's station. He keeps an eye on the fusion reactors, problems with power flows, damaged areas of the ship and all that other good stuff engineers do. This is also where he took away power from Bren's weapons in Awakening, so he distributes power too.
Navigation: Yuna's specialty. She basically drives the ship--in and out of hyperspace, through solar systems, and around objects and planets of interest. It's the steering wheel, the driver's seat.
The On-Board computer: Zak's domain, of course. He has full access to all of Gen's subroutines, modules, and programming through his computer terminal.
Weapons/tactical: Bren is the only one that's ever been seen at this console, and I bet he'd never let anyone else do it. =D It controls the canons, the guns, and all the other defense systems on the ship.
Communications: Gret works here. She monitors the communications channels on Deepwater and between Deepwater and other ships or planets. Since the sensor controls are nearby, she'll take those occasionally.
Environmental controls: the only function here we've seen so far is to launch the lifepods (and that's only useful when you're not sitting in the lifepod, right? =D), so Lise also does sensor-duty a lot if she's on the Command Deck at all. I bet this is where you'd go if your chamber was getting a little chilly at night, though. =D
I picked the Command Deck as the sitemap for one easy reason--this site was DESIGNED to be complicated, and there had to be something familiar as a roadmap. This is it.
An interesting thing about the set used for the Command Deck--it was built on top of a pit full of tires and scaffolding, so that when the ship rocks, the actors have to move with it--no faking needed here. =D
Technically, the Habitat is not a seperate deck from the Command Deck--they are actually on the same one [Deck 4's supposed to have metal grids or something] and are next to each other. But, like with the Bio Room, I decided to be flexible.
The Habitat is a hanging-out place--most of the time, they eat there, since it's next to the Kitchen with the food synth. Sometimes they do their little independent projects there (like Lise was at the end of Cycles; and Bren in Lullaby), and it's where they spend their coffee breaks when they feel like getting out of the intense, office-like atmosphere of the Command Deck.
They've also been known to play a game in there every once in a while (Infestation); do mission briefings and interrogations (Reflections and Refugee); have meetings and discussions (Hunt and Awakening); and view mission records (Lullaby and Reflections). A bit like the Observation Lounge on the Enterprise, except you're allowed to put your feet up.
I used it as a place for updates and stuff, and I kinda forgot why (I used it on the old version). =D
On the Deepwater, Gen's biocore is supposed to be on Deck 5. Gen's biocore is supposed to be the place where her bioneural components are kept, and where the programming and cyberneural implants interact with those components.
Originally, I had Deck 5 pegged for Mission Records, but I decided to change it because I thought the terminal would fit better with the biocore than the records.
The Gene Bank is the centre of Deepwater's entire purpose--they are supposed to deliver it to Earth, maintain it during the trip, and safely implement it when they get there. We haven't actually seen into the Gene Bank, although we did get a glimpse into the matrix storage area once (Infestation). The Gene Bank is more than just gene samples, though--inside are thousands of cloning capsules growing the samples into clones the same way the crew had been grown. The Gene Bank is a self-contained shuttle that can pass through an atmosphere, so once the detach sequence is initiated, it pretty much takes care of the landing part.
This is also a pretty obvious deck--they're quarters. They sleep in them, they prex in them (Legacy, Fugue, Aurora), they go there to be alone. It's their personal spaces. Zak's the only one that really works in his, tapping away at his computer terminal most of the time. It's unknown whether the quarters are actually all on the same deck.
This deck does not actually exist on the ship--all I have to say. It's actually a function of the Habitat, and that's probably why the episode guide was there in the previous version of the site--it just became too hard to find after a while.
Deepwater's weapons bay is loaded with guns and weaponry to prevent against boarding and for hand-to-hand combat, and the ship's defensive capabilities include 4 quantum resonance canons and guns. The placement of this weapons deck is probably pretty accurate to the actual ship.
Its shield generator is used to protect the ship from fire or any other things that can damage the ship. Since the hull is pretty weak from the last 500 years, the shields are a very important part of Deepwater's defense.
When I was about 50% completed with the site, I decided that the cancellation deserved its own section on my page--it wasn't a piece of passing news for the Habitat, it was really important--so I created the weapons deck. I decided to group it with the shields because that was also important enough for its own deck, and those just seemed to go hand-in-hand.
The Shuttle Bay contains two shuttles, Shuttle Alpha and Shuttle Beta, which are used for transportation between Deepwater, and other ships and planets. The shuttles are relatively small, with no hyperdrive, shields, or weapons, big enough for about 9 or 10 people--but most of the time only 2 or 3 of them leave the ship at one time. The Shuttle Bay has an airlock connected to it, which contains the crew's shuttle gear.
Shuttles, transportation, links to other sites--I think you get it. =D
Well, those are all the decks and parts of the ship. Some of them I just sorta made up for my site, but that's basically it.