In a medium size mixing bowl combine the flour, baking soda, and salt, mix until well combined
In another large bowl using a handheld mixer, cream butter, brown, and white sugars together on medium speed until smooth
On low speed mix in eggs, peanut butter, and vanilla. Turn the speed to high and blend until light and smooth (about 3 minutes)
Turn mixer to low speed, gradually add dry ingredients until well combined, and dough forms
Cover tightly and refrigerate for 30 minutes. Preheat oven to 350 degrees F. Using a tablespoon, roll dough into balls, place balls on a large piece of parchment, add one peanut butter cup to half of the balls, gently press another ball over the peanut butter cup, sandwiching the peanut butter cup between the two balls of dough. Roll the stuffed dough into a ball insuring all edges are sealed
Bake the cookies on a non-stick cookie sheet for 10-11 minutes or golden brown. Allow to cool on the cookie sheet for 8-10 minutes before transferring to serving plate.