I have 2 kayaks, 1 is an Old Town Loon 120 (I think) and the other is a Perception Acadia (both are roughly 8 yrs old). Both are sit in kayaks. We go fishing all the time in them, typically with a lot of gear. The cockpit in the Old Town is great, very large. My usual arrangement would be like this,
In front of boat (inside) - room enough for a large size waterproof bag or other storage device (this would be shoved all the way to the front of the boat, next in line just between the knees you have room for another storage device or in your case a good sized tackle box.
Behind the seat (inside) - room enough for another large storage container or in the case of my last trip there was room enough for 2 x 2.5gal water containers, tarps or a few other small items.
In front of boat (on top) - bungee cords hold another mid-sized storage container and I use the extra slack to hold 1 or both of my poles.
If the fishing is bad and I decide to do more close to shore exploring I can take the poles off the top and run 1 down each side of the boat on the inside with the reels sitting just next to the seat.
Here is a pic of my bro-in-law from my last trip, 9 days on the brazos with fishing equipment.
http://www.putfile.com/pic.php?img=6184082