I had a Sea Eagle SE8 and in the time I owned it mistakenly punctured it 2 times, which believe me was pretty hard to do.
To patch it I used 2 different methods.
The first is that I had a patch kit from Intex that I used. About $10 from Meijer. It had patch material and adhesive. I roughed up the area around the hole with sandpaper, put the adhesive around it, waited a few seconds for it to get tacky, then placed the patch on the hole. Since the hull was deflated, I put a large landscaping brick on top of it, let it sit overnight, then sealed around the patch with gorilla glue the next morning. I never worried about it again, and that thing never leaked again.
The second one was a quick patch, and not nearly as strong looking, I wasn't as confident in it. I found the leak after stowing the boat in my trunk, the C-connectors on my MinnKota just punched a tiny hole in it. I didn't have much in the way of a patch kit, just the kind you'd use to get back to your car. I roughed it with my knife, put down some super glue, and stuck a piece of vinyl on it. After it dried a few seconds I inflated the boat and surprisingly it held very well.
That said, I would've rather used the true patch kit. I felt better about it, and it looked a heckuva lot better. But neither patch ever failed.
I'm not sure how FlexSeal would work. You have to plug the hole somehow, so I'm not sure if FS would actually plug it -vs- just create a seal. Plus it might look kind of wonky since it's a spray.
I loved that boat though, it was super fun to use, I just wanted to do some kayak tournaments around me that don't allow motors, and since my SE8 basically required rowing, it was next to impossible in the wind, so I had to use something more paddle friendly.
Good luck!