IIRC, on this Yost Kidarka, I put on a few coats of polyurethane varnish, painted on the (traditional PNW) designs, then put on another coat of varnish. I don't think the last coat was necessary.
In fact, I've painted designs on lots of kayaks, with lots of coatings, and there are no real issues - don't overthink it, just do it!
Rustoleum works fine. So do spray paints - though I do tend to go with the better (more expensive), tougher variety if I can.

Good luck!