Make sure you have a way of making things handy. I used a plastic milk crate with short lengths of PVC pipe bolted to it to hold a net and a spare rod. I also put my lunch and any other items I wanted into the crate. I used four stretchy ropes (sorry forgot the names) to hold it down. One other thing is to make some kind of cord to hold onto your rod and the paddle. I used curled phone wire with either velcro or a small clamp on either end. You can get clips at any hardware store to clamp down on the cord and make loops. It's funny how a paddle or rod can get away from you when you are paying attention to something else. Some people put a gallon soap (Tide) bottle on the end of the anchor rope. You can always toss the bottle out and chase after a large fish if there is any chance of it wrapping around your anchor rope. There are kayak fishing web sites that show pictures of how to rig your kayak.
Don't forget to wear a personal flotation device and sun screen.
East Bay Ed
I also fish from a sit-inside yak. Mine has slots to rest the paddle cross-wise, but I find it gets in the way, so I rigged a bungee on the side so I can trap the paddle lengthwise (quickly, with one hand, in case the other has a rod w/ fish on).
I stow my net under a bungee on the bow, within arms reach, but again, out of the way.
For flies and small fishing gear, a vest was the only way to go for me. If I stowed it somewhere on the yak, it would just get spread around everywhere.
I usually carry rods in the cockpit, pointing rearwards (and I only snag the spare with a stray cast about once every trip).
Oh yeah, I rigged a drift sock with the idea of trolling in the wind, but I rarely use it. Still, it's there under the hatch.
I'll take a look at the boat when I get home to see if there's anything I forgot.
OK, there's more:
An extra length of the rope you use for rigging, a knife to cut it with, and a lighter to seal the ends. Plus, you know the tools you used to do all this stuff? Bring a few with you in the car, when you go fishing. Just 'cause...
I've already got a cord attaching my paddle to the boat, of course, but I'm soon adding a cord to attach to whatever rod I'm fishing with. Don't ask me why...
I've read that people have used a spray skirt like a striping basket to avoid tangles with their line. Sounds like you gentlemen are leaving the cockpit open to access more gear. What do you do with your striped in line?
Check out this Florida-based website => http://paddle-fishing.com/. You can find a lot of great ideas for rigging your yak in the Forum. I have a Heritage Red Fisher sit-on-top I bought when I lived in Orlando. Yak fishing is very popular, particularly in-shore.
One thing to consider if you are going out in the Sound - get radar reflective tape so ships will pick you up on their radar (West Marine has em). No fun getting swamped by a tanker or a tug pulling a barge! Put a change of clothes in a dry bag, stow it forward. Get an aft mounted light so you can be seen in early am or later pm.
Here's mine. Note how I have my rubber mesh boat net propped in front of me as a rod holder for when I'm trolling. I don't think any fish could yank my rod out of the boat before I can grab it, since the hoop always catches the reel. I've had 'em run a little line out before I could grab the rod, though. The handle of my net is resting on a small soft cooler positioned under the bow thwart. My rod rests on either of my thighs, pointing out the back, allowing me to paddle and troll at the same time, and easily grab the rod.
Note the rod-holder bases behind my seat, for when I'm trolling with gear. That's my anchor trolley running from bow to stern.
I can attach my anchor line to the stainless ring, or stake through the ring into the mud bottom or a mud bank with my combo wading staff/stakeout pole.