Yeah, I know, an extended midtower with an mATX motherboard sounds strange. But this demonstrates the flexibility of an mATX motherboard along with the "big boy" capability of this board, it is just as at home in a large case as it is in a small form factor case. Of course, the large case must support mATX form factor, but most do.
First observe the "keys" on the CPU pins to orient it correctly and carefully install the CPU into the CPU socket. Prep the CPU heatspreader by cleaning with isopropyl alcohol and a lint free cloth.
Prep the CPU cooler by cleaning the base with isopropyl alcohol and a lint free cloth. Apply thermal compound to the CPU surface per manufacturer's instructions. (if using a CPU cooler designed that the heatpipes directly touch the CPU surface, you should spread the thermal compound with a credit card or other thin flat object as the cooler base will not spread the compound properly).
Install the CPU cooler and memory.
Install the motherboard into the case. When using a large CPU cooler you may want to plug in the ATX12v cable before placing the motherboard into the case. Wire things up, install the video card (if using one) and any other PCI cards you may be using. Double check your work, and you're done.