None of my cables were clipped to the joists and I've just laid them on top of the insulation but sounds like in the other thread people thought that was ok as the joist could conduct some heat away.
I don't suppose it matters too much which side they're flush against. I would suggest whatever...
I've just done the same (rockwool between joists) but underneath my floor as I'm a first floor flat. Given I couldn't guarantee my neighbour wouldn't put halogens in (even though they're not sold anymore) I decided it was best to use thermalhoods over the downlighters and then insulate around...