Even with the right cooling VRM temps can be an issue. I ran a watercooled PC with 10 fans for a bit and that one had crashes due to VRM temp issues, even on a more expensive board. Reason? Dead spots in airflow. And that NH-D15 will suck up a lot of air around it. It may not be an issue, but those VRM coolers may also help if you do decide to pick up a better CPU that fits the motherboard in a few years maybe (if that is on your mind)
I/O is the In/Out on the back of the motherboard, so USB ports and such. It's easy to get a USB splitter and if you get a decent one they're fine, but any devices that need good throughput or low latency (like your keyboard and mouse) should 100% be plugged into your PC.