When you are in parallel, all the feed wires come to the controller as separate feeds... you probably should use a bus where you connect all the feeds - THEN a single wire feeds those to the controller. Refer to the (nicely detailed, by the way) diagram posted by taylorbob1.
Notice also in the diagram that the battery negative post is grounded to the chassis. Therefore, you DO NOT ground the negative panel terminals to chassis. The charge controller is merely an intermediate component in a larger DC circuit... in which the battery is the termination point. Current generated by the panels FLOWS THROUGH the charge controller, is regulated, then flows into the storage batteries.
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