Preheat your oven to 300 degrees F. In a medium bowl, whisk together the flour, baking soda, and salt.
In the bowl of an electric mixer on medium speed, blend the sugars and butter until you get a grainy consistency. Add the eggs, peanut butter, and vanilla, and beat until fluffy. On low speed, add the flour mixture and peanut butter chips, and mix until barely combined.
Fold the dough together a bit with a spatula, and drop heaping tablespoons onto a parchment-lined baking sheet, 2 inches apart. Add a small spoonful of jam on top of each cookie, and use a toothpick to swirl the jam into the dough.
Bake each batch for 18 to 20 minutes, or just until the edges of the cookies are lightly browned.