It is designed to run passively. The provided fan is only if you are in a tight area where air is low or if you overclock your CPU to 2.0GHz instead of 1.6GHz. I don't know what HDD you can to use... but it may need metal (touching metal case) or heatsink. On my setup.. I put the HDD on suspension.. in a fan less design, and the HDD overheats and locks up the computer when the HDD is heavy in use for a long period of time. A heatsink (fanless) solved the problem and a low 120mm speed case fan. So yea the problem was not the CPU/GPU overheating but the HDD
Don't forget that: - The model you selected has a PSU outside (like a laptop PSU), so no need for room required in the case for one. - You'll need a hole for the wireless antenna, which comes with the board. I mention the above as I don't see them on your sketch.