Hi Geoff,
I come from an inshore, flats fishing background. That means most of the fish I catch are less than .75 meter and weigh 15 lbs (kilos?) or less. The largest fish I have caught have been from a sea kayak and include 100+ lb tarpon and 100+ lb sharks. In the case of these large fish, I never make any attempt to get them in (or on) the sea kayak. One large 5-6 ft shark grabbed a lure of mine and I got him up to the boat twice. I was about to reach down and try to get the lure when it came loose--lucky for me. Sharks are very dangerous, and in such circumstances, will snap at your hand if it appears in their eyesight. My advice for sharks is to waste the lure, cut the line. In the case above, I wanted the lure because I was in the 2nd day of a weeklong trip, and it was the only large lure I had. It was intended for tarpon--you will lose the lure with tarpon also, but not your hand.Â
Some fish, I consider dangerous and try to avoid. For example, barracuda (& sharks to a lesser degree) will jump out of the water, presumably in an effort to attack their tormentor. You do not want to be in front of the business end of a flying barracuda.
If I am fishing from my Hobie Adventure or AI, I always carry a net big enough to hold the fish I intend to catch--it usually works (you still catch sharks, but usually they cut or break the nylon line before they get to be a problem.)
There are several people on this discussion who do go after big fish in deep water. AlohaDan, in Hawaii, is one such person. So you should look at his posts. Other people, perhaps less experienced than A-Dan, also are attempting deep sea fishing--just keep checking this discussion and look at some of the earlier topics.
Here is a link to a very interesting day fishing out of Destin, Florida. Check out the videos in that discussion.
http://www.hobiecat.com/community/viewtopic.php?t=9548
Where to put the fish? Again, that is going to vary from person to person. When I am in a sea kayak (covered cockpit), I just chuck them in the cockpit between my legs. When I am using my Adventure, they either go in a cooler behind my seat or a thermal bag behing my seat or into the hull via the center hatch. The Hobie Adventure or AI is a much more convenient fishing machine than a sea kayak.
Keith