One neat thing is that kayaks are great to access skinny water, and fly fishing is a shallow water presentation. So, great, right? I started on the Susquehanna for obvious reasons.
You will learn that "Less is more" for kayak fly fishing. I haven't done it much the last few years, minus a few forays into bluegill/small largemouth. No projections, knobs, handles, crevices....whatever. Anything will snag your fly line. Steve Gibson is a kayak fishing guide in Sarasota that I have gone out with many times. He uses NuCanoe now, and it has a very 'clean' deck. Less (never nothing, right?) to catch fly line.
Keep your line in the boat as much as you can. If you're right handed, it's dang near impossible when you're stripping line turned hard to left.
Unless you're catching little fish on little flies, set the hook by stripping, not with the rod. I know this is, again, dang near impossible. It helped me to pull both my rod hand (right) straight back and to the right while pulling the line hand back to the left. It's just totally harder to get a good hook set sitting in a kayak, so you have to focus on that.
The river I fish for smallies holds most active fish up along the bank, like mostly in the first 4 feet. Despite my expectation of line management nightmares, I found that I could drift along at casting distance and lift my line after stripping those productive 4 feet. Pitch. Strip. Lift. Pitch. Strip. Lift. You can cover a lot of water and not have to reel all the way back to the boat. The stripped line just floats along beside you. Easy. I haven't done this for a few years because the fishing has not been very productive. It's hard enough with spin tackle. Spin/fly isn't a bad way to go. It's what we do in the bay in FLA. If the bite is good, ditch the spin gear and get 'em on the fly. I may start fly/kayak fishing again this year. The largemouth fishing on my local lake has been exceptional this year.
There are other kayak flyfishing tips that would pertain to specific waters and conditions. Whenever you run into anything puzzling, post again.
Syl