I did a HAF 932 case mod last year. Ventilation, air flow, and cooling are outstanding. I installed the original Coolermaster Hyper 212 with two Scythe S-Flex 1600rpm fans in normal front to back orientation. The cpu heatsink and fans lined up perfectly with the fan on the rear panel. The results were outstanding.
I took a look at the motherboard you selected. There is a tall blue colored heatsink just below the cpu socket. I am not positive but it appears it might be tall enough to interfere with the 212 in a bottom to top orientation.