First make sure you've jailbroken your phone and then enabled SSH. (There are tutorials everywhere for this) Also, install WinterBoard from Cydia.
Then, open your SSH client on your computer. (I recommend WinSCP for PC, and Cyberduck for Mac). Choose SSH as the protocol in Cyberduck or WinSCP, then type the IP address of your phone. (You find this in Wifi Settings) The default credentials are username: root password: alpine
Once logged in, navigate to /var/stash/
From there, you'll see a directory called Themes.XXXXX with the X's varying from phone to phone. Upload your theme into that folder.
Now, respring your phone and then open WinterBoard. Your theme should appear in the list. Select it, and it will respring your phone, and there you go!