I have my MIB things wrapped in acid free tissue paper, and then stored in small, sturdy plastic boxes. The top of the box has a very small hole drilled in it, and I have silica packs inside. Probably 3 boxes fit in one plastic box.
If I had something that was MOC with a bubble, I'd probably custom make a foam protector to go around the bubble-- to keep it from shifting or smashing. (I've seen something I've seen for 80s camera/lenses). I'd still use acid free tissue paper though to go inbetween.