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Best Fuse Location? Answered

Please note that the best place for the main in-line fuse is AS CLOSE AS REASONABLY POSSIBLE (in terms of cable length, not just proximity) to the positive terminal of the battery (or battery bank).

Placing that main fuse right before the motor controller will absolutely protect the controller, itself, but battery cable between the battery terminal and the main fuse is entirely unprotected, so minimizing that length of cable is a must for safety.