Hi Simon
I think the method is to turn the boat upside down, put the boards in with one or two layers of plastic shopping bag wrapped around them where the board meets the boat. Then you push some thick epoxy filler into the gap and wait for it to set - make sure the boards are pointing straight forwards while the epoxy sets.
Take the boards out and fair in the filler.
There may be other refinements to this process - I've only replaced bits of filler like this. I've never done the whole lot.
Most Mozzies seem to be done this way, though I wonder why more are not set up with a much bigger gap between the board and the case (like 2-3mm) so some sort of hard felt or similar material could be put in there. This would surely end up putting less scratches in the boards. Anyone know why Mozzies don't do this?