how I did my build: first mount the CPU, RAM and then the CPU cooler onto the motherboard. Now your cooler (like mine) probably will block some ports so they're not that easily reached, but believe me it's easier doing such a cooler outside the case than inside it, and then using some tweezers or something to connect the audio and fan connectors (if they happen to be overlapped by the heatsink). Once you have this you might as well plug in the power from the PSU and test start it (short the power pins) with a HDMI from the motherboard to see it POSTs.
Then it's time to put it in the case. You can mount the motherboard (don't forget the IO shield), then all the case connectors. Add the fans and connect them too. Add all the drives where you want them and SATA cables. Now, the HDD cage has two "hotswap connectors" pre-mounted (basically an extension of SATA and SATA power secured in place), I happen to use those but if you won't, you can unscrew them and use your SATA and SATA Power cables directly (you need 90 degree connectors), it reduces the amount of stuff at the back significantly. Add PSU cables as you go, naturally. I installed my graphic card last, and routed the PCI power connectors last, through the back so they run under the card.
Hope this helps
Edited by ExplosiveMachin - 1/24/16 at 1:58pm