Kayaks are pretty seaworthy, sit-on-tops are just about unsinkable. That said, dealing with anything more than a 1-foot chop in a flat-bottomed lake boat is really no fun. If you find yourself caught out in rough water, try to keep the bow or stern pointed into the waves, or within 30 degrees of perpendicular, even if you have to take a roundabout course. Do not run parallel to the waves.
Boat wakes are also a threat. Most boats give no thought to anyone else, at least not anyone smaller than them, and will plow by without even looking at you. Always watch out for boat wakes, and turn into them like waves. When dealing with motorboats and jet-skis, I just assume they are drunk and not paying attention to anything. It hasn't failed me yet.
Crossing a boat channel is like crossing the highway: look both ways, wait for a good time, and do it as fast as you can. You do not have right-of-way. Unlike an automobile, a boat doesn't have brakes, and if you do something stupid, it will run right over you.
