In a large microwave safe bowl, heat the butter until just melted. Stir in the peanut butter, brown sugar, baking soda and salt. Whisk in the eggs and vanilla extract; then the oats. Stir in the flour, and then stir in the chocolate chips and peanut butter cups. Cover and refrigerate for about an hour, until the dough has firmed up a bit.
Preheat the oven to 350 degrees F. Line baking sheets with parchment paper.
Scoop out heaping tablespoons or use a 2 inch cookie scoop. Roll cookie dough into balls and place on cookie sheets 2 inches apart. Use the bottom of a drinking glass to gently press down a little. Press additional chocolate chips into the tops, if you'd like.
Bake 11 to 14 minutes, or until the cookies are slightly firm to the touch in the center. Transfer cookies to a rack to cool completely. Store in a covered container for up to 1 week. They can be frozen for up to 4 weeks.
Notes
You can certainly use 2 cups all purpose flour in this recipe instead of using any whole wheat flour.
Mini Peanut Butter Cups can be found in a bag in the candy aisle of major markets.