You are supposed to have a fuse in series with each panel wired in parallel. This is normally done with a "combiner box". These can contain fuses or breakers. MidNite solar, Outback, and others make combiner boxes.
#6 wire should be plenty from the combiner box to the charge controller. It should also be fine from the controller to the batteries. You will need a fuse or breaker in the positive wire near where it connects to the battery. 60 amp would be appropriate for the #6 wire.
It's not necessary to have a fuse or breaker between the combiner box and the charge controller but it makes it nice for servicing. If you don't have one you have to turn off the combiner breakers to kill the input to the charge controller.