Preheat the oven to 350° F. Line a baking sheet with parchment paper.
Stir together the flour, oats, cocoa powder, baking soda, baking powder, and salt. Hold this aside.
Blend together the butter, brown sugar, and granulated sugar in the bowl of a stand mixer, or in a large bowl with a hand mixer, until the mixture is smooth. Add in the eggs one at a time, mixing after each addition. Blend in the vanilla extract.
Mix the dry ingredients into the wet mixture in two or three additions, scraping down the sides of the bowl once or twice.
Place the bowl of dough in the fridge for 30 minutes to chill. This helps the baked cookies keep their shape.
Bake the cookies:
Use a medium cookie scoop (about 1 ½ tablespoons size) to scoop portions of chilled dough onto the baking sheet, spacing them two inches apart.
Bake the cookies for 13-15 minutes, until the edges of the cookies are set. Remove them to a cooling rack.
Add the peanut butter cups:
As soon as the cookies are on the cooling rack, gently press a mini peanut butter cup into the center of each cookie. The hot cookies will begin to soften the candies.
Add the eyes:
After about 5 minutes, the peanut butter cups should be soft. Gently press a large candy eyeball on top of each peanut butter cup. Press the eye down just a little so the peanut butter cup collapses a bit, and gets smooshy around the edges.
Continue baking:
Continue to scoop out and bake the rest of the cookies, adding peanut butter cups to the baked cookies when they're hot from the oven. And eyeballs once the candies are soft.
The cooled cookies can be served immediately. They can be stored once the peanut butter cups are no longer melty.
Place the cookies in a wrapped or sealed container, along with a slice of bread to help keep them soft. Store them for up to 3 days.
Notes
Don't let the butter for the cookie dough get too soft - it should give just a little when pressed.