Layered cheesecake is always undercooked. How to fix for future cheesecakes?

I made an apple crisp cheesecake yesterday in a 9" pan. 3 chopped apples on top of the cheesecake, and the crisp topping on top of that. Baked it at 350 for 35 minutes per the instructions. The edges had good texture but the middle is runny. This seems to always happen when I bake layered cheesecakes. Could use some advice.