This is a tedious and somewhat difficult process, so be prepared to have space, time and patience. Most trailers are just sheets of overlapped aluminum sheet goods, so you will need to obtain the proper gauge and colored sheet goods to start with. Many have square drive screws, so if yours has rivets, I would suggest being prepared to drill them out and replace with good quality stainless screws.
The frame of the trailer is really just a steel box, so carefully remove the damaged skins by removing or drilling out the old screws and rivets. Use the old sheets as templates to cut the new. Carefully replace them methodically throughout the trailer, using weatherstrip and waterproof sealants as needed at all seams. Always overlap seams downward (like siding) and rearward so that wind driven rain flows naturally down and aft, not into the seams.
If your trailer is in really bad shape, you are probably better of just selling it and getting new.
Also, you may find that just putting a new lower panel over or under (cut out perforated piece and place new under flap) the good pieces will work. You could also do this using thinner aluminum diamond plate for a nicer look. My trailer just had rot down low so that's what I did then repainted the faded upper.
Good luck!
Jeb, April 2007