Preheat oven to 350 degrees. In a large bowl, combine the flour, baking soda, baking powder, and salt. Set aside.
In a large bowl, beat the butter and the peanut butter together until fluffy. Add the sugars and beat until smooth.
Add the egg and mix well.
Add the milk and the vanilla extract.
Add the flour mixture and beat thoroughly.
Make the dough into balls (about 1 1/2 tablespoons or a traditional-sized cookie scoop) then place onto an ungreased cookie sheet, leaving several inches between for expansion.
Using the handle of a wooden spoon or your thumb, press a hole into the top of each ball. Do not flatten out. Keep the dough round. It will expand.
Place about 1/2 teaspoon of jelly into each hole so the jelly just fits in the hole.
Bake for 10-12 minutes. Do not overbake. Cookies may appear to be underdone, but they are not.
Cool the cookies on the baking sheet for a few minutes, then remove to a rack to cool completely.