I'm planning on building a new x99 pc very soon as was wondering what your thoughts are on motherboard cooling. I will be running a custom loop but was wondering what your thoughts are on blocks for the VRM and chipset. My (very limited) understanding is that boards are designed for a stock cpu cooler/fan to also provide the airflow to help board cooling. Wouldnt replacing the stock item with a water block or even a high end air cooler impede the ability for the board to cool? Having good caseflow obviously would help but im wondering if it would be as efficient as stock design? Just want to get some peoples thoughts before i decide which avenue to take.
I do not know about efficient, but it is certainly more effective as long as you know exactly what you are getting into. The board will be fine, don't worry about it. If boards do anything well, they cool themselves very effectively.
Watercooling WILL NOT make a system more quite, nor will it make a system put off less heat, in fact it will put off more because that heat is being carried away from the internals more effectively. The reason the included fan is the way it is, is because it is not a matter of efficient, it is a matter of cost. It is likely the LOWEST cost solution that will function properly. Water cooled boards are far better at displacing heat.
"Wouldnt replacing the stock item with a water block or even a high end air cooler impede the ability for the board to cool? Having good caseflow obviously would help but im wondering if it would be as efficient as stock design?" no, it will not impede the cases ability to cool, if it did, the aftermarket providers would not sell very well. Often CPUs do not even ship with a cooler. So, for many people, the included cooler is just something to get them by until they get a better one.
Blocks for the VRM and chipset....Motherboard manufacturers are VERY good at using sufficient cooling stock on their boards. using anything other than a CPU/GPU cooler, is usually pointless. Even RAM water blocks are generally thought to be pointless.