I believe the bottom hangar is the one they use. It is much closer to the street so it'd be easier to access. The one exception might be the long distance shot they used in "Knight to King's Pawn" (when Billy, Zoe, and Mike were trying to break back into the abandoned SSC through a secret...

"Don't Stop the Knight"; The amusement park where Michael has to deliver Gunner Haas to Ivana Alexandrovna in exchange for "the box". Don't Stop the Knight1.jpg The white roller-coaster structure is the "Colossus" and the one to the right is "Scream" The place...