If the fabric is dacron, and the paints and glues vinyl-based, I think your first suggestion has merit. Whatever you use needs to be flexible, though, and also needs to protect against UV degradation of the underlying fabric.
I was faced with a half-dozen areas of paint damage on my rebuild project. What starts as a half-dollar sized spot in reality was pretty extensive. I kept peeling off large sections of paint, which was not adhering to the underlying fabric. If the paint is bubbling and sloughing off, you really need to remove it until you get to an edge where the paint is no longer peeling.
Once you have located the sound edge of the area, you'll need to build up the now depressed and ugly section. My Citabria uses the "Poly" system, so I brushed by hand several coats of Poly-Spray, the silver stuff, and feathered the edges between coats with 320 wet/dry paper, used wet. When it had built up enough, I shot some color, and if done right, you can barely see the repair.
For very small areas, I used a putty knife and some epoxy to both build up and secure/stabilize the damage. Epoxy sticks to everything, and if you mix in some micro-balloons or some other filler, it sands and handles better.
If you've got some paint-chipped areas, and want to secure the edge, try some MEK with a small rag. The MEK dissolves and removes the vinyl-based paints, and turns a thick, chipped-paint edge into a smoother and thinner area, which again you can build up with some Poly-spray (if using the poly system), then shoot the color.
