I assume both batteries are connected to a battery switch, yes?
The answer is - which ever one will start the engine!
However, both batteries should be connected with the same size wires - unless there is no battery switch. If there is no switch, then I would have to guess that the smaller battery, with the thicker leads, is meant for the engine and the larger battery with the thin leads is for the "house" (navigation and other lights, stereo, GPS, etc) electrics.
Dan
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