Sometimes your stator and/or voltage regulator can fry itself because it is not designed to output the kind of load required to charge a deep cycle batteries Your original cranking batteries will get topped off pretty quickly by your outboard charging system but two deep cycles require more amperage over a longer time.
Also, it is possible that you had a loose wire on your charging system and this caused the resistance which caused the melt down.
Sorry this happened. I have experienced it personally and it sucks.
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