The orientation of your CPU cooler can affect airflow and cooling efficiency.
The orientation of your CPU cooler can affect airflow and cooling efficiency.
Make sure they can be flipped and just swap the fan positions.
You have options, but neither setup is perfect. Placing intake at the top and exhaust at the bottom pushes warm air toward the GPU, while swapping them reverses the flow, pulling cool air away from it—both can cause heat buildup. It might be worth testing both configurations to find the optimal temperatures for your CPU and GPU.
Keep the top case fan in place. Changing it might improve airflow, but it could also pull air away from the front intake before it reaches the CPU fans. You'd need to test this yourself.