When I install Dropbox on a new machine, I can use selective sync to decide which folders are kept in sync on that machine. You can configure selective sync in CLI mode using 'dropbox exclude <path>'. (Unfortunately, I don't think there's a whitelist option.)
Is there a reason this wouldn't work for your use case?
I don't want my personal account on the server in case it was compromised. Besides, even if you use that "dropbox exclude" command, the client will start downloading all of your files when you first link it and there's no way to tell it not to do that before you have the chance to do all of your excludes.
Is there a reason this wouldn't work for your use case?