The one immediately aft of the sail is the Lockout truck, and the one at the aft of the ship above the engine room represent the logistical escape truck. The lockout is used by Navy Seals to enter and exit the ship at sea while submerged. The logistical escape truck can be used in-port and expanded to load equipment into the engineroom. However, I believe it was designed for the SEAL delivery vehicle.
That’s correct, the new Virginias do have a lock-out chamber there just aft of the sail. The Ohio SSGN conversion can use up to four of the old Trident tubes for lock-outs for the SEALS. The others (and usually the second pair too) are all capable of carrying up to 154 Tomohawk missiles.
Of course the Virginia’s do not have those large tubes, but they can launch up to 12 Tomahawks themselves.
I believe the most aft location is also used for helos, and I believe, from a greater height, the other one aft of the sail can be too, they just have to maintain a height great enough to ensure that there is no chance for rotor issues.
My son-in-law is a career submariner. I have been priveledged to be on board nuclear subs to meet XOs and COs a number of times. Next time I do, I will ask specifically...or, I’ll simply ask my son-in-law.