RE: How to...
For painting MonoKote or any film covering.
1. Scuff the surface with 0000 steel wool OR the green pot scrubbing pads. Be careful you do not go through the covering on the "high points" - ribs, etc.
2. What you want is a "frosted" appearance on the covering.
3. THOROUGHLY clean the area(s) with rubbing alcohol or denatured alcohol.
4. Prime
5. Mask and paint.
6. If the paint is not fuel proof, clear coat it. I have found the water base polyurethane is definitely fuel proof to 10% nitro and several reports indicate it is good to 15% nitro.
For ggogmo
You do not need to put anything on the cowl before applying the MonoKote, although many people would suggest a coat of BalsaRite over the cowl.
I have a suggestion which may be easier in the long run. Why not paint the cowl ? Bring a sample of the color you need and have it matched in latex paint (about $10 a quart ). Put a coat of sanding sealer on the cowl, sand, then prime. Spray your latex and let it "cure" - typically 7 - 10 days, then clear coat with a water base polyurethane to fuel proof it. There are several threads here on painting with latex.