I put the back seats down, place a plastic tarpaulin type cover in place then lay the bike on there usually with the front wheel off as mentioned. Fit's in a treat and doesn't usually move around, thus making it drama free.
A mate has the more expensive Thule R/R on his 1996 Mini Cooper and it works wonders. He rates it. It's bizarre seeing a disassembled bike on the backseats and a bike on top of a late Mk1 Mini