I've used such rigs and i solve the problem thusly .... I carry a couple of blocks of wood that are a little bigger than the wheels, and sit them (aligned front-to-back) on the cabinet below, just inside the wheels, rendering the wheels a few millimetres above the cab below. When the top cabinet is in place, push the blocks outwards until they hit the wheels, which will usually help stop any rattle from the wheels while playing. I use smaller blocks if i have a head sitting on a cabinet with a large handle.
If the cabinets are in good condition, you can glue or staple some carpet around the wooden blocks to protect the tolex.
As to having the amp on it's side, I've also done that and it's never caused any problems. It is a good idea to check that the tubes are well-seated occasionally if you're doing this regularly.
