you need new bed sides, your only seeing what't turned into a $1,500 to $2,000 repair job.
In order to fix this right and never have it come back again you must do what I did.
-buy new bedsides patches. $150 bucks
-cut old bedside out vivet and them on do all body work and paint.
the problem is the inner skin has a "C" channel which keeps all the slop in there. when you are inthere you must coat everything with a protective coating. You can use eastwoods internal frame coating. I did this when we fixed my bed and sprayed every sq in of the underside of the bed. Then I did a graveltex coating which is kinda like bed liner under then entire truck and wheel wells but it is not rubber in case I ever need to do a repair. (had a friend who runs a auto restore shop recommend it since its he own blend of wanna be Line-X)
you need to put wheel well liners in also, they about $150 new from morpar.
if you have bubbles in you bed you will also see some prob in a few years in your rocker panels...same issues...and the inside of your frame will roat inside out lol.
RAM tough, but crappy however.
Hope this helps ya, I spend 5 grand so far redoing every inches of my truck so it can never rust again and coated my frame inside and out.
fender flairs will just make your problem worse and only cover your rea issue up for about a year or two max.
This is a fixed bed which had all the same damage...it cost me $2,000. a new bed will not do anything for ya but rust out again. 02-08 were not good bed designs.