The VC-25 747s (i.e. the current Air Force One aircraft) have stairs down to the cargo deck for ready access in flight (it's been nearly 30 years, but IIRC there were two - one in the front and one aft of the center wing box). There is also a fancy retracting stairway that permits SLF to climb up to the lower deck then take the stairway to the main and upper decks.
Among other things there was chilled storage on the lower deck for the galley (the VC-25 aircraft have a full kitchen - not the 'heat and eat' capabilities of most airliner galleys), as well as access to the EE bay.
However I don't believe the lower deck had any seating or was approved to be occupied during takeoff/landing.