Panel lines and Rivets
I saw one of the Hangar 9 P51 ARF's this summer that a guy used some sort of marker and also airbrushed some smoke & weathering, but he didn't clear-coat it. Looked awesome for a film-covered ARF, but I don't know how it will hold up to glow-fuel. It was his maiden flight, so it hadn't been through the mill yet.
There are a couple guys in my club that claim they have had great success painting solid colors on Monokote, after they lightly scuffed it up with a sanding sponge. But, I don't know what kind of paint they used.
When all else fails... test! You could just make a simple rectangular "frame" out of balsa, then cover it with whatever film you intend to use and heat-stretch it the same way you would if you were building the plane. Then scuff it up, draw your panel lines, shoot your clear and let it cure. After a few days or so, test it against some glow fuel and see how it reacts.
I definitely would stay away from "burning" flat rivets in with a brass tube like you do on glassed planes. Don't know about using glue dots for raised rivets on film... not sure whether they would want to "pop off" when/if the film flexes. I suppose you could test that along with the paint.
Neo