Map Locations I added (for their function):
Positions from the BS2 Atlantic Express map were combined (and AE extended to rest of Rapture).
Lighthouse (positioned) proximity to Welcome Center and to Mt Ryan (as its supported by rocks built up on the top close to the surface).
Mt Ryan - the underwater 'Sea Mount' mass of solid rock that protects Rapture from icebergs (as its top areas are at less than 100 feet depth which is above where all the highest buildings in rapture stop - generally 600-100 foot depth)
Fumerole Alley - chemical industry site, collecting various chemicals from the geothermal vents in that region of the map.
Industria - A general location for more than a few large industrial/manufacturing/warehousing installation that are largely caverns/tunnels in the solid rock of Mt Ryan.
The Shallows - an area on Mt Ryan that is about 100 feet depth. Site of extensive SeaWeed farms (that need light from surface) and of industries that use ALOT of air (which they can access easily at those shallow depths) -- including the Cities garbage incinerators. Rapture's Sewage plant also located here so that the 'nutrients' assist in the SeaWeed farms yields.
Vulcans Forge - marshalling center for a majority of Rapture power/utility generation (never was that monstrocity in Hephaestus that was built more for show and quickly had its capacity exceeded as the City grew). A large field of Geothermal Power units surround this loctation. Hephaestus does have the main desalinization and heat pipe units for the City.
Port of Rapture - The main submarine access to Rapture (used much more when Rapture was being built and when Surface goods and materials were still being brought in enmasse.
Submarine Yard (and Sub-Canal) - underground Repair/Construction/Storage facilities for undersea craft (and component assembly for the city construction). The underground Canal links the facilities to Port of Rapture.
Hermes Mall - from someone elses online suggestions for a location of many of the businesses we see advertised, close in to the 'ritzy' part of Rapture.
Ceres Green - Center of the central farming district (near Arcadia) with its many underground (tunnel/cavern) farms (electric grow-lights and heating, more than a little hydroponics...) Home of the 'frankentree' plantations used to recycle Raptures Oxygen.
Minervas Den (corresponding to online speculated of where this was)
Atlantic Express lines heading off-map to other industrial sites (mining, quarrying minerals, and more farms)
The Abyss - sudden deep drop (more than the gradual slope down to the 1000-2000 foot depth of the seabed surrounding the area of the ancient underwater volcano Rapture is built on). Was a volcanic core magma chamber that collapsed long ago. Weird glowing down there made Persephone a tourist attraction before it became a prison/asylum.
Smuggler Tram added - Smugglers Den is nowhere near Arcadia, though in BS1 you walk thru a tunnel and you are there. Solution: Smugglers (Fontaine) used a mile long tram tunnel to transport contraband to Arcadia - a good central location in Rapture and which offered nice secluded spots for clandestine transactions for smuggled goods (and proximity to Farmers Market and the adjacent farming establishments). If you look at Smugglers Den in BS1 you will see alot of infrastructure was 'secretly' constructed to facilitate the major smuggling operation (kind of hard to justify why Ryan's men couldnt find this place long before Fontaine got his Splicer Army).
Freight Yard - unmarked tracks shown on the BS2 AE map are freight train storage tracks. When not in use, freight cars used on the Atlantic Express system have to be stored or sorted to make into trains going to different locations. Freight traffic usually was run at night so as to not block progress of the faster Passenger Train activities. Proximity to the AE Depot is logical.
Additional Bathysphere routes will likely be added (a competing company to the Austen) to make the full system a little more complete and convienently interconnected.
The red circles are only abstract locations and dont actually present the masses of building and interconnected 'streets' linking them (many of the levels named sprawl across the seabed). There are likely many more (plaza/squares) connected by the street system than those shown (from BS1/BS2)