at the moment i just put everything in separately. with virgin blue they dont care so much. qantas is another story though... i am getting a neil pryde all in one bag so ill just need to take that and the board.
I recently flew Air NZ. they were pretty cool too. they give extra allowance for sporting gear as long as the bags arn't over 2.5M long.
Board in board bag - I wrapt my board in bubble wrap befor puting in the bag and contoured some heavy cardboard around the nose and tail -no damage, and like staffan said don't forget to remove/loosen the vent plug. I would put your disasemble the boom and put it in the board bag. Fellow travellers also took a quiver bags with special pockets for masts, with them but you'd be surprised at how heavy the get taged the bags fragile and top load only - not sure if the bagage handlers can read though, from what i saw anyway. Try travelling with the least gear you can - 3 sails max and one boom that covers the range.so theres still harness/base/extension/wetty/gath-hat/fins screw drives etc all to pack as well. If you have some spare time on your hands at your destination (day only each side of trravel) send the gear in advance through freight department of the same airline company your travelling with, and pick it up from their freight depot when you arrive, saves a lot of hassles at the airport. BTW the freight companies are usually only open 9to5 weekdays so you would need plan your arrival/departure itienary base on this if you where to go down this path.