I wouldn't get a fiberglass tonneau cover if you would be constantly removing it. That would be a pain.
They have cloth ones that roll up to the back window that work pretty well.
Also, if you don't have a bed liner, I would get one or a bed mat so that the rods don't get scratched up.
Or you could always just put them in the cab.
I have an extended cab Ranger and the rods fit in the cab just fine, but sometimes I open up the back window if the rod is too long.