If your poles are 2 pieces, they will fit in your box with a topper or tonneau no problem.. but most of my casting rods are one piece and will not fit...
I have an ARE topper on my truck mostly for the puppies.. but also for gear. I open the windows of the topper and truck and the casting poles sit in the box an push through a bit into the cab. As someone pointed out.. most of the time all the rods are in the boat.
The next question you likely will have... isn't it really noisy with the windows open to the topper...
I use a bicycle inner tube slightly inflated to seal the wind from the windows... works spectacular.
This is my setup.. fish poles on each side.. casting rods in the middle.. the gaps on each side is where the dog creates sit.. gear underneath, etc.. its not a pretty, but its very functional.