Lower oven temp to 325 degrees.
Add 1-2 inches of warm water to a roasting pan or large rimmed cookie sheet and place on the bottom oven rack. Allow it to heat up for 5-10 minutes before baking your cheesecake.
In a stand mixer fitted with the paddle attachment or a hand mixer, beat the softened cream cheese until smooth. Scrape down the bowl once complete.
Add sugar, peanut butter, vanilla extract, flour and salt. Beat on high until smooth. Scrape down the bowl once complete.
Add in eggs, one at a time, beating on low after each addition until combined. Do not over beat.
Pour HALF of the filling over the cookie crust. Use a spatula to gently smooth it out.
Evenly place full-sized Reese's Peanut Butter Cups throughout the pan (16-18 will likely fit).
Pour the remaining cheesecake batter over the top of the peanut butter cups. Carefully spread the batter so that it evenly covers them.
Cover the bottom of the outside of the spring-form pan with aluminum foil in case of leaks.
Bake for 60-75 minutes, or until there is a 3-4 inch jiggle in the center. Then turn off the oven and leave the cheesecake in the oven for another 1-2 hours or until the oven has cooled to room temperature.
Remove the cheesecake from the oven and let it cool completely to room temperature (another 1-2 hours), then place it in the refrigerator overnight to set.
Remove the spring form once the cheesecake has cooled to room temperature or after chilling overnight. Run a butter knife around the edges of the pan to loosen it first.