Before beginning any prep protect the glass with safe release painters masking tape.
First thing to do is clean off the wax from all of the polishing. This will take a solvent to get a clean surface. A liquid sander like Paso will do this or use mineral spirits.
Next, sand all of the wood surfaces. Using a medium/fine sanding sponge rough up all areas needing paint. Wipe off the dust with a clean rag.
Now you can prime the window with an oil base wood primer.
That's it. The key is getting all of the wax off from the polish and sanding.