I have 2 large tool boxes in my '09
the back one is a custom built box
the front one came from TransferFlow, it has a 30 gallon gas tank & toolbox combo
Both are in bed boxes, both have Rectangular Steel tube between the toolbox & bed, to allow the debris to be hosed out.
The tops of the boxes are almost flush mounted to the bed rails, allowing me to have a tonneau cover
Some people like the bed rail mounted type, they allow you to put tools like shovels, etc. under the tool box