We use the egg crate foam type mattress topper on the upper bunk and it works fine for our adult daughter - it also stays up there when closed.  With regard to the lower bunk, we use the thinner type foam padding as an extra insulator over the seat and cushion and it seems to work fine for us.  You're right about how the lower seat and foam extension gets kind of stiff after many, many years of use.

  Sharon & Bob Mendonca
  88 Vanagon GL
  88 Westy