Heat your oven to 350°F. Line a cookie sheet with parchment paper.
In a mixing bowl, combine the vegan butter with the peanut butter. Use a mixer and beat on medium speed until light and fluffy, about 2 minutes. Add the sugars and beat for another minute.
Add the vanilla and the flax egg. Stir into butter mixture. Set aside.
In a separate bowl, combine the flours, cocoa, baking soda, baking powder, and salt. Whisk to combine. Pour the flour mixture into the wet mixture. Stir to combine. If the dough seems too crumbly at this point, add 1 tablespoon at a time (up to 4) of plant-based milk and stir to combine.
Add most of the chocolate chips, reserving ¼ cup for the final step.
Drop cookie dough balls by rounded tablespoonful (using a cookie dough dispenser helps make the cookies evenly sizeonto your prepared baking sheet, leaving about 2 inches between each and press a little to flatten.
Bake for 8 to 10 minutes. Remove the cookies from the oven and place and transfer to a wire rack to cool completely.
Once the cookies have cooled, melt the reserved ¼ cup of chocolate chips in the microwave (for about 11 seconds, then stir), and using a butter knife or other utensil, place a dollop of melted chocolate on the cookie, followed by a Skittle. Do 3 to 4 per cookie, with different colors. I avoided using the red ones, to keep with more Halloween colors. Add two googly eyes to each cookie. You may want to get the back of each eye wet to help you press them into the cookie so they'll stay put. Alternatively, you could use a little bit of icing to achieve the same end.