The rod system automatically assigns the best rod to your lures to maximize your potential catches. However, if you wish to change the rod assignment to a custom one, here is an explanation:

You can assign specific fish lures to your rods. This will help you build rods for catching specific fish. To do so you will have to go to the rod screen, pick up the rod you would like to assign a lure to, and then tap the Assign button in the lower right corner of the window. A new, lure-picking window will appear.

These lures will be assigned to the selected rod.

When the assigned fish is chosen on the lure selection screen, a designated rod is automatically equipped.

The basic rod will have every available lure from the fishery automatically assigned to it. Picking a lure unassigned to any other rod will equip a basic fishery rod.

One lure can only be assigned to each rod. Attaching a previously-assigned lure to another rod will unassign it from the previous one.