I also fish out of a 16 ft boat. We converted the seats so they have storage units underneith. Keep fire extinguishers, extra cannonballs and tackleboxes in them. For bait I use an old coffee can and keep that in the back corner of the boat (can't trip over it there). I screwed 5 pieces of pvc to the back wall and we keep extra rods there and the net when we are running. It (the net) gets in the way when fighting fish so I keep that upfront with the handle sticking out so I can quickly grab it. Filet knife and spare oars (always carry oars) in the gunwells and that's about it.
For tackle boxes I like the hard plastic ones because alot of the gear I carry has sharp hooks on heavy jigs and it tears up soft stuff. Also try carrying 3 20 oz. weights in a soft box. Not pretty. The fish finder is on the passenger side right behind the front windshield on a swivel mount. This is a good spot because you can see it from the back or the drivers seat.