I'm always doing it over USB since I find it faster and easier to just plug it. There are tools out there made to synchronize a local folder with a USB folder (for windows there is SyncToy : http://www.microsoft.com/download/en/details.aspx?displaylan... ) so if you don't mind plugging your phone to sync it this could be a very easy way to sync multiple folders on your device.
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I'm always doing it over USB since I find it faster and easier to just plug it. There are tools out there made to synchronize a local folder with a USB folder (for windows there is SyncToy : http://www.microsoft.com/download/en/details.aspx?displaylan... ) so if you don't mind plugging your phone to sync it this could be a very easy way to sync multiple folders on your device.