Make sure you backup everything you want to keep, once you get the new motherboard plug everything in and boot from your windows DVD/USB. When choosing where to install it delete the old Windows partitions and create a new one.
If you are using the same windows serial you might need to deactivate it.
http://answers.microsoft.com/en-us/windows/forum/windows_8-windows_install/windows-8-product-key-deactivation-guide/6c5245de-8516-4c99-95fe-0fb458d849e5