Preheat the oven to 325ºF.
While the crust is cooling, prepare the filling. Place the cream cheese into the bowl of a stand mixer. Mix using a whip attachment for 4 to 5 minutes or until the cream cheese is light and fluffy.
Add the granulated sugar, brown sugar, cinnamon, nutmeg, cloves and vanilla to the whipped cream cheese and cream together until well combined. Use a spatula to scrape down the sides.
Next, add the eggs one at a time until combined. Set aside.
To assemble the cheesecake, pour 1 cup of the caramel sauce on top of the cooled crust. Spread it around leaving a ½-inch border around the edge of the crust. Add the apple slices, spreading them out to evenly cover the crust. Pour the cheesecake batter over the apples.
Place the cheesecake pan onto a cookie sheet with sides and place in the oven. Pour 1 inch of hot water into the cookie sheet.
Bake for 1 hour and 10 minutes at 325ºF. When the cheesecake is done, turn off the oven and crack the oven door open and allow the cheesecake to sit for 30 minutes. You do this to make sure the top of your cheesecake doesn't crack due to a sudden change in temperature.
Remove the cheesecake from the oven and refrigerate the cheesecake for at least 5 hours to set.
Spoon the remaining caramel sauce over the top before serving.