Ubuntu One is a synchronizing tool, not a backup tool. The principle of synchronizing is that all computers have the same files. The principle of backing up data is to keep data stored in case of emergency.
In Ubuntu One every file you delete on your local computer will instantly be deleted on the cloud version of your data as well.
Backup solutions based on Ubuntu One are not flawless. Here are two options you might consider, though I advise against them:
You could add a folder to Ubuntu One. Once that folder is synchronized to the cloud, you could decide to stop syncing it on your local machine (unmark it in the Ubuntu One interface). This is prone to errors.
You could also make backups locally and store those in the Ubuntu One cloud. Again, though, if you delete the backup locally, the cloud will follow because that is what clouds do.