By default, the folder named 'Ubuntu One' serves as the root folder for the
So when displaying your U1 files through https://one.ubuntu.com/files/, everything residing in this folder (including subfolders) is synced, and additionally synced folders (e.g. ~/mybackup/subfolder, see
u1sdtool --list-folders) appear as links/subfolders under this root with the title 'My synced folders' folder there.
For some reason this might not be displayed consistently across all clients, I noticed that e.g. the current Android client shows additionally synced folders as a sibling of the root folder.
Note that it is possible (as of 12.04, maybe earlier as well?) to change that root folder to another folder within your home as described in this answer but make sure you know what you are doing and stop the syncdaemon prior to any changes through
u1sdtool --quit (and start it again afterwards).
After doing so, I was able to remove that folder safely and use another one of my choice instead.