You will be forced to run them in single channel if you use this cooler.
Modern CPUs are faster than most RAM available on the market. This means that if you take away the extra bandwidth offered by a multi-channel architecture, then the CPU may be kept waiting for data from RAM, even if all it needs to do is to load it into L2 cache (or vice versa).
Each color DIMM slot on that motherboard is a channel. You have two channels of up to two DIMMs.
I strongly recommend getting a cooler that will not cover the DIMM slots.