You have a recreational yak like me, which is perfect for fishing anything but heavy surf. I have a Pungo 12 & a Perception 12.5, and I turned them into the "angler editions".
OK, nice and simple, a few mods will make your day.
#1) Add a paddle holder. No need to be fighting your paddle with a fish on. Should cost under $20 bucks. (I like the ones that Pungo puts on the "angler edition"). Remember to use small STAINLESS bolts, loc-tite on the threads, and grind off excess/sharp edges. This mod may take you a whole 15 minutes at most.
#2) Add a rod holder. I used a circle saw kit along with a plastic through hull rod holder, and some stainless screws to secure it. (Don't over tighten with screw gun, take your time) Remember to cut with the mindset that the rod holders go on a slant, and you want the rod to stick out behind you. This mod might take a whole 25 minutes, because you will spend 24 minutes thinking "holy crap, I'm, cutting a hole in my kayak", and 1 min for the installation.
Some folks add the rod holder that mounts on top of the deck to the front, I had one on my last yak, but haven't missed it.
#3) Go to Chinese restaurant and order a small egg drop or wonton soup. Eat soup, wash container, store bait in container. Perfect for leaving it between your legs while you fish, you can bait up quickly. Cost - about $1.75 plus you get a meal. Time depends on how hot soup is.
#4) Buy small plastic tackle tray with compartments (one lid, the clear plastic kind) that is no more than 14" x 10". Store essential items in there - lures, hooks, sinkers, etc. No need for a big tackle box, just a small but usable selection of stuff.
#5) Wear cargo shorts with big pockets. In here I keep pliers, nail clipper, knife, hook degorger, or any combo there of, they are all in easy reach when I need them.
Other thoughts, if tackling big nasty fish, keep a hand held gaff in the bungees on the bow of the yak. Comes in handy for big bluefish, jacks, shark, etc. I also shove a 5 gallon bucket from Home Depot behind my seat, fits perfectly and makes a great fishwell.
I can take pics of my stuff if my descriptions don't give you enough of an idea. I think there are a couple of basic shots of my 'yaks in the "Kayak fishing surprise" thread from a few weeks ago. Let us know how you make out.