It's not uncommon to have two batteries in a boat. The most well known use is a two "bank" utilizing one for starting and the other for "house" duty. That is running your electronics, lights, pumps etc. The standard method is to have a dedicated starting battery (high amperage delivered in short burst) and a house battery that allows for deep cycling (discharge) for the items mentioned above. These two batteries are connected through a switch which allows you to select what battery you wish to use and also if needed, to combine the two for emergency starting power.
Usually the two are placed fairly close to one another mainly for wiring convenience and ease of service. Some members relocate them to the center console (if space allows). I've also seen them mounted on each side of the stern. CCPs did this as well as some EX models.
Speaking of mounting, I would bet that the battery box is mounted to the deck in the console to keep the battery from sliding around. That's why it doesn't move. You are correct in that lifting the battery out of the box when place under the console takes some arm strength and twisting. Like one of those Chinese wood puzzles.
Take some pics and post up what you have so we can better see what's going on with both batteries.
Good luck.
