Someone has added the second battery box under the hood, probably to improve cranking due to poor connections or too-small battery cables. It's also possible they left the under-floor box empty. Are the cable clamps under the floor insulated, maybe with tape or some other way of preventing the hot cable from shorting out? If the under hood battery box is big enough, a battery bigger than the Group 1 under the floorboard with more cranking amps might have been used.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
Cringe and wail in fear, Eloi- - - - -we Morlocks are on the hunt!
There is nothing noble in being superior to your fellow man; true nobility is being superior to your former self. - Ernest Hemingway
Love your enemies and drive 'em nuts!