I was wondering is you can have bed rail caps and a tool box on top of them.

 

Yes you can, and the tool box will still attach normally.

 

So i would just bolt down the tool box on top of the rail caps?

 

Just like this.

 

There is almost no difference.

Step 1: Install bed rail caps

Step 2: Set toolbox on top where you want to mount it

Step 3: Drill hole through toolbox, bed cap, and bed rail simultaneously

Step 4: Put bolt through hole and tighten down with a lock washer or nylon lock nut