This is something I just did. I had one bunk bad and just replaced all four. I lucked out and got a great deal on the carpet from another forum's member for the cost of shipping.
To get the boat in the air, I built a platform using concrete blocks, needed them anyway, then capped that with a couple of 2 x 12 scaffold plank I had laying around and shimmed with scrap wood. Before I built the platform, I lowered the nose of the trailer as low as I could. I then built the platform and jacked it up as high as I could, this lifted the back off the trailer. I then built another platform for the front and then lowered the trailer and the entire boat was then off the trailer by about 2-4". Depending where I was working on the trailer, I had to raise or lower the trailer to get some clearance at times, but it worked great.
Someone else had suggested, after the fact, that they just placed 2x material across the members on the trailer and jacked up the boat one side at a time. Which way is better, is debatable....his seemed very simple, but the boat is only held up by a jack, so keep head, arms, hands, etc out from under places. With my method, my boat was going no where and couldn't fall. I had supports that needed straightening and my hands were in bad places at times, so for me, my method was safer in my mind!
The water method is of course preferred, if you are very close to water.
One other thing I did was replace my 2x4 bunks with 2x6 bunks and she sits much nicer on the trailer, but haven't tried loading or unloading yet. I'm assuming that should be better as well!
Seems like a big task, but amazingly easy!