That is what I do now, but it would be so much easier to do it from the backend of WB. Then I don't have to have the FTP information ready when I want to make a backup and, since I have made quite a couple of sites using WB, it takes a while to find all the correct info.
You could just load a copy of OPENRSM CloudBackup onto your server.... I'm doing that on a bunch of my WB sites right now and it works just fine.