I would use a rooftop combiner box and use one run of two wires down to the controller. Even if you chose to run all eight or four down to the controller, they will have to be ganged either on a bus, at the controller's terminals, or at a common interrupter before the controller.
By using a combiner box you'll have the opportunity of less wire loss and can use a manual circuit breaker before the controller. The latter makes it easy to remove power from the modules to the controller and rest of the system when working on the 12V system.
I made my own combiner box and I should make them for the market since the solar folks want a pretty fair amount for them. They are just a weatherproof box with bus terminals inside.