1. Plug your USB with the windows 8.1 install file
2. Start up your pc and enter into your BIOS
3. Go to your boot priorities and make sure the hard drive you want the OS installed on is your first boot priority. Then underneath that somewhere should be your USB as well, if it is then it's fine.
4. If that is all in order you can go back and under boot override select your USB this will boot your system from the USB and the windows 8 installation guide should come up
5. In your installation pick "custom installation" if you want to pick the hard drive that it should install on to.
Hope this helps! There are different ways I believe but hope this is what you are looking for