Ugh...
Dammit...
It's both my first post and I subscribed to this forum specifically for this topic too...
/Sigh...
I'm sorry Daryk but I think your internals are a bit off.
A lot in fact.
From the available lore, It it explicitly stated that each Mech had it's own bay door. We also know that Manatee was originally a civilian cargo hauler design that was kludged to create a stopgap solution, meaning it didn't have any of the more advanced (ie currently standard) specialized tech & gear like drop-capsules and automated mech-repair assistance systems.
In fact, the only modifications that we can be completely certain of are the installment of 4 Mech gantries in the cargo hold, the enlarged weaponry suite and the enlarged long term living spaces for a total of 8 crew and 4 MechWarriors from the original of 5.
Lastly we have this image;

Based on these data points, I created a mock-up in KSP to visually illustrate my points;
Aspect 1;

Aspect2;

Aspect 3;

Here are my assumptions;
Manatee has at least 4 cargo doors* based on the lore; Assuming it was originally a container hauler, specialized in quick turnarounds, I think it was a simple symmetrical design with triple cross-arch design for structural integrity and 6 doors.
*Represented by the radiator panels with green lighted batteries under them
Based on my engine and engineering volume guesstimates , don't think there is enough space under the cargo hold area to fit these components. In fact, I think the cargo hold doesn't actually cover the whole floor but is actually a donut shaped area with a pillar in the center, which houses the reactor and engineering spaces.
Since each Mech Cradle is supposed to hold a Mackie, The Cargo hold ceiling should be somewhere between 14 to 18 meters high. (The pure white area in the mock-up) The engines probably eat at least 6+3(internal) meters under the hold, leaving about 10 meters for the Gun deck (Striped Area), Command deck and Avionics (Orange Cone).
Since this was originally a cargo hauler, it's quite probable that the cargo hold's ceiling had a circular rail track & an overhead crane setup by default for internal rearrangements. I think they increased the number of cranes on the ceiling track to 2 in the militarized version:
Door 1 (Left door in the first picture); Mech Cradle 1-1
Door 2:(Right Door in the first, Left door in the second picture) Mech Cradle 1-2
Door 3:(Right Door in the second, Left door in the third picture) Cargo 1
Door 4: Mech Cradle 2-1
Door 5: Mech Cradle 2-2
Door 6: Cargo 2
Each Cargo zone holds the spares and consumables for the advent Mechs, 2 cranes allow using each pile and service 2 mechs for max efficiency.
The Gun deck houses 4 weapon installations (represented by the RCS thrusters), 2 escape pods (represented by the external barrels) and 2 aux sensor/comm installations (represented by the antennas, or maybe 1 aux and one engineering airlock) as well as life support and pantry. The whole layout is done in the standard onion / armoured core style meaning the more critical a system is, the closer to the middle it is placed.
The Bridge deck has the bridge, living quarters, galley, sickbay and so on.
The armoured citadel design mentality also continues here; the bridge is in the middle, surrounded by living quarters with various other areas lifting design tips from medieval castle design to create defensible choke-points in the event of boarding, ladders for easy movement down but the only stairway being clockwise and so on...
Avionics level has the avionics hardware, main sensors, prow weapon installation and any aux. fluid tank or other noncritical mass that might work as ablative armour in case of a bad encounter.
Again, sorry to start off with a criticizing post but what do you guys think?