We've had a recent litter of 9 pups and 6 of them have been flown interstate - they all cope pretty well (I'm sure they cope better than I do - worried grandma, all the time!).
With the crate, you would normally have the option of a hire crate or outright purchase of the crate when the travel is organised - but it will depend on who is organising the transport and through which company. If you want to purchase a crate to keep and your breeder is arranging the transport, then make sure that they know to organise transport with a purchase crate instead of a hire crate.
If you are going with the hire crate option, then you will remove your puppy and any toy/bedding that belongs to him from the crate and leave the crate at the freight location where you pickup the pup - you won't take it with you at all
Location will depend on who is flying the pup - Virgin or Qantas - each will have their own freight depots at the airport where you will pickup the pup. Once the flight lands, the pup will be unloaded with the rest of the cargo and then delivered over to the appropriate freight depot for collection by you
Yes, when your puppy is home along and in his pen, setup a toilet area in the pen for him - if he's used to pee pads, then I would (at least initially) stick to doing the same thing. He might not always get it right to start with, but if he's already trained to pee pads, then you should find that he will mostly toilet in his little pee pad toilet area that you make for him