In general case you upload your videos via the Flash Uploader of Youtube. That might be a good way sometimes, but if you do this very often, interruptions of the upload may occur. It should be your decision how to upload those gigabytes of data. Currently Youtube doesn't support raw FTP upload. But your server does! And if the Youtube servers are slow that evening, it's your servers 'problem'. Once the files are uploaded to your VPS you can do whatever you want, the server will upload the files independently from your computer.