Line a baking sheet or work surface with parchment paper.
Place the yellow melting chocolate in a microwave-safe bowl. Microwave in 30-second intervals, stirring after each interval, until smooth.
Pour the melted yellow coating into a tall cup.
Hold each waffle cone by its tip and dip it open-side down into the yellow coating. Shake off the excess and place it open-side down on the parchment paper. Let the cones set for 6–7 minutes.
Melt the white melting chocolate in 30-second intervals, stirring until smooth.
Dip the open end of each cone approximately ½ inch into the white coating. Shake off the excess and allow it to set for 4–5 minutes.
Reserve some of the white coating, transfer it to a piping bag, and cut a small opening at the tip.
Slice each cupcake horizontally. Press the bottom half into the cone.
Pipe white coating around the cone opening. Place the cupcake top over the opening and press gently to secure it. Let it set for approximately 5 minutes.
If desired, pipe thin decorative lines across the white section.
Melt the chocolate chips in 15–20-second intervals, stirring until smooth.
Dip the pointed tip of each cone into the melted chocolate.
Place the finished pencils on the parchment paper and allow them to set for 3–4 minutes before serving.