Just the way you do. Well, almost. I lay down what I call a rough clear first, which means it may have a bit of orange peel texture to it. Let it dry thoroughly. Wet sand it with a 400 grit or fine (wet) steel wool. That will give your finish coat something to bite on and help level some of the paint seams. I also believe it helps prevent runs.
I try and do it in good light and at an angle (which changes during painting, depending on which part of the rocket you're on) where you can see the paint going on. When you see it build up and it hits "flash-point," stop. Immediately. Try and be fairly quick about it. It's easiest to see this on the fins 'cause they're flat, but you can detect it on the tube as well—it's all in your angle to the light. Practice on a flat surface and you will be able to see what I mean by "flash-point." When all the orange peel is gone and the paint has built-up to a glassy sheet, it will flash at you like a mirror. Again, be quick. Don't linger.
I generally start with the bottom edges of the fins, then outboard fin edges, then body tube and nose and then hit the flat parts and leading edges of the fins.
This method is not fool-proof (which is unfortunate for me), but with practice, you'll see your clear-coats get better and better. My big problem is I'll think I'm "almost" there and then hit it again or "it's perfect except for this one little spot." I've learned to stop there (mostly). If it really bugs me, either from a run or a bit of peel, I'll wet sand and do it again. But I really don't like to.
I hope someone posts a better way, because I'd like to know it.