Hi,
If you want to take backups of Deduplication Storage Folder, you need to browse through your BE Media server, under "Shadow copy components", "User data", you'll find your Dedup folder;
Just select that resource and create your backup job/policy.
Ps. If haven't changed on BE 2010 R2, you can only run Full backups of your Deduplication Storage Folder. Might want to consider running duplication jobs of your backup jobs targeted to Deduplication Storage Folder, it depends how large your Dedup Storage is, how much you have tapes and so on...