I bought the tray holder system tht holds 4 large plano traysfor about $130 from Cabellas and installed it in my console above my feet.1 tray holds all my hooks and swivels, 1 tray holds my meduim rapalas and hoochies, one all my iron jigs, and the last holds 8 12" tuna plugs.
I then bought 7 clear plastic shoe boxes (Walmart, Home Depot-Sterilite brand) with lock down stackable lids, and put them in my electronics box to one side of the radio. I bought about 30 1 gallon zip lock freezer bags and placed the lures and hooks in each clear bag to keep them seperate, untangled, completly dry, and visible inside the shoe boxes.1 box is for planers, trolling sinkers and birds, 1 for hoochy daisy chains, 1 for leader material, 1 for tied leaders and bait rigging stuff, and 2 for are for the big marlin lures. All of this stuff stays on the boat.
I then put a 54 quart ice chest under the leaning post for warm sandwiches, 2 GPS's, fish finder, hand pliers, rod belts, knives, etc that all fit with room to spare and I leave the drain plug open.
This dry ice box, the ice chest with my fillets, and the rods are the only things that come off the boat in the afternoon, and are also quick to load in the morning.