Andy-
I prefer the right way up. The standard RS gunwale hung triangulated trolley protects the boat and is a solid stable base for it. The axle width matches roof bars nicely. That way you can also fit everything in it; 3 rigs, 3 sails and 2 foils fit nicely in their bags leaving the car clutter free.
In USA smaller 'dollies' are often used rather than the standard RS trolley and they may then need the boat to go upside down on its gunwales instead. If you do turn it upside down be sure to have some good fat padding on the roof bars to protect the decks and do not over ratchet it tight.
Ivor-
Unloading; This is easier. The same process in reverse but without the lift up.
Securing; Once you have tied the boat to the trolley amidships and at the bow before lifting (then easy to lift as one, with or without helpers) you then just need to tie the trolley to the car/rack.
I tie 4 places; each side of the axle at the rear roof bar, across the front roof bar and then the front of the trolley to the front of the car. If any one of those 4 points fail due to a chafe it will still be pretty solid.