here is how I have always done it.
once you decide who your buying from, go to your dealer whom will do the transfer, get a signed (in ink) copy of his federal firearms liscense, send it with payment, your gun will be shipped to the address on the lisence with a copy of the FFL from the sender, sender needs an ffl to ship to, receiver needs an FFL to register the firearm. you fill out the yellow sheet when you pick it up.
RR
edited to add: the only thing that has to go through an FFL is the part with the serial number, the action, the lower (in the case of an AR-15), or a complete firearm.