I too fish from a kayak and while it takes some practice, it's not difficult at all. Just focus on the basics of fly casting and then practice sitting down on a stool like other mentioned. You'll get the hang of it pretty quick. Lot of great basic fly casting instruction is available on YouTube.

As for kayaks...A NuCanoe Frontier is great until you have to paddle one back up river to your truck. But for straight out stability, they're hard to beat. For the fishing I do around here, I love my Jackson Kilroy.