I did a clean install of Ubuntu Natty. Now I can't get UbuntuOne to sync my files. The files are in UbuntuOne I can read them. Previously I installed Natty Beta 2 and everything worked fine. It seems like it was automatic.
If you setup your computer with Ubuntu One then it should sync all the files in your Ubuntu One folder automatically and allow you to select which "cloud folders" you want to sync under the "Cloud Folders" tab in the Ubuntu One Control Panel.
We were having problems with one of our servers that was impacting some users from either connecting to the service reliably or syncing files in a timely manner. We've got this under better control now so that should no longer be an issue if your account was on that particular server.