Assuming you have full SSH access to the WebFaction server (you should according to the WebFaction features page), I suggest you try following the detailled instructions found here. If you get stuck on any step, then you can ask a more specific question (probably better to ask on serverfault though).
The fact that the repository is on a remote server does not really change anything. You connect through SSH to the remote server (WebFaction) and you follow the steps as if it was a local machine.