Fractal Desing Meshify S2 Fan Setup
I wouldn't bother with the third fan in the front. You will have to remove the small hatch in the PSU shroud and the fan will then be blowing most of its air into said PSU shroud instead of the inside of the case. That third fan slot is only useful if you plan to use a 360mm radiator in the front.
The included GP-14 fans are quiet and move a good amount of air. I'm using a pair of GP-14s and a GP-12 in my secondary rig's Define C and after about 5k hours of power-on time I am not noticing an increase in sound compared to when they were new. Of course if you plan to upgrade the fans it would be easier to do so right away.
As for cooler orientation: If you let the cooler blow towards the rear, you can keep the top closed which helps to reduce noise. You may have to raise the cooler's front fan a bit to clear the RAM sticks.
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