If you want to do a complete clean install, backup any important files elsewhere that you don't want to be deleted.
There a good guide on isntalling window 8:
http://www.overclock.net/t/1240779/seans-windows-8-install-optimization-guide-for-ssds-hdds
Before you install windows 8.1. I would download the motherboard drivers from here:
http://www.gigabyte.com/products/product-page.aspx?pid=3915#dl
You only need the Audio, Lan and chipset. Download them to a USB thumb drive.
I would unplug any drives that won't be the boot drive.
Boot up the Window 8.1 setup. Either via disk or USB drive depending on your method.
You can choose to do it in MBR or GPT format, look at the guide linked.
When you get to the screen to choose where to install the OS, I would delete the old partitions containing the old OS. Then you can click on "New" to create a new partition for the OS to be installed on.
After you installed window 8.1, it will restart and you configured the settings, you will be greeted to either the Start screen or desktop. You can now plug in the USB thumb drive containing the drivers. Install them all. You may need to extract them and go into the folder to find the Setup.exe.
Afterwards, you can run Window Update or you can use WSUS Offline updater.
http://download.wsusoffline.net/