How do you paint over beeswax?

It depends on how much wax there is. Are you talking about small amounts, like crayon marks? You can try removing it with a solvent like Goo Gone. There are some primers that claim to work over glossy surfaces, including crayon marks. Check with your local paint store or home improvement store. Look for brands like Kilz or Zinsser Bulls-Eye 1-2-3. Read the back of the paint cans to see what these primers will cover.