Welcome to ExPo kpredator!
All the above posts are great advice.
I would add that once you have everything installed/set up the way you want, climb into the truck bed, close the hatch and tailgate
(during the daytime), and look for ANY spots where daylight is showing through.
These will also be the places dust, drafts, and water will get in.
When I had my ATFP I used a combo of bulb seal, a Bedrug, tailgate gaskets, and copious amounts of RTV silicone throughout.
If you get aggressive about sealing it up, you shouldn't have any further issues.