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The batteries and proper wiring are an issue in themselves. Actually, you don't even want three cables direct to the batteries. You install one high amperage fuse ON each battery, and the positive cables go to those. Those fuses are designed to save your boat from a "crowbar short", i.e. a massive short that otherwise could set the electrical system on fire with the full power of the batteries. Those two positive cables go to your battery switch, then to the distribution panel (fuses or breakers) and everything else gets connected there. WIth the arguable exception of the bilge pump, which many people run straight to the battery.
Your first priority after pumping out the boat, is probably to find out why it flooded. Whether you took rain in through an open port, or a cockpit drain got blocked and it ran in the companionway, or you've got a leak below the waterline. You need to find out what that was and fix it.
After you fix it, you'll need to fix or replace the bilge pump. Since bilge pumps and float switches are notorious for failing, I'd suggest TWO of each, separate. And a counter or hour meter on them, so you can tell if the bilge has been cycling while you are not there. That could have killed your battery if nothing else is wrong.
On thing at a time, first dry out the boat and see what else the water may have damaged. You'll need to dry it out VERY THOROUGHLY, using fans, dessicant buckets, or goldenrods (heaters) to prevent the moisture in the floor and fittings from causing a mildew infestation. Possibly a mildecide to help make sure that doesn't happen.