Thanks for all the input, didn't really think it mattered too much, I am however keeping the rock (rubble mostly) and sand separate in the fuge. Mainly so they're live little pieces for frags that aren't buried in sand! Not really a fan of the frag on a plug look. Just wanted to make sure I wasn't missing anything.
I'm thinking maybe the rock first personally as it gives more 'pockets' to catch bigger particles, the chaeto will float above both sections of rock and sand to help filter as well. Hopefully too, with rock then sand... rock can't flow into sand if disturbed, as easily