On the wall of the bed near the cab there are two knock-out covers.What are they for as mine were missing when i got the truck.
thanks

 

I had mine out when I put in my liner. On a 2004 they have 4 clips that hold them on and a rubber gasket that seals the hole. The back side is open to the elements.

The only reason I can see for them is if you have a cap or cover on the bed - the rubber seals will keep any rain water from splashing up from under the truck and getting into the bed. If you don't have a cap/cover then the inside of the bed is already wet and they don't matter. Unless you are carrying small things that could fall through the hole.

Here is a picture of mine

 

So how do you get them back in. I took one out and I can't get it back in all the way. 2006.

 

if yours is like my 2004 then just push and the clips will pop over the sheet metal and hold it in. I think I had to push kinda hard on one side in order to compress the rubber gasket.

How did you remove it? Did you reach around from underneath the squeeze the clips, or did you just pry it out? Did the little clips get broken? If the clips are broken, you'll probably need a new cover.