
Bake the colors only until the top layer is mostly melted and smooth. It can take anywhere from 10-15 minutes at about 250 so just keep an eye on it. Baking time depends on how full they are, the brand of crayons, and more.
Try to mix and match colors so they look appealing when the layers merge.
You can even use silicone molds instead of muffin pans, but make sure to place your silicone molds on top of a foil lined cookie sheet when you put them in the oven, so the silicone itself does not melt.