Best practices for MS deduplicated volumes as backup repository:
1) It is important to format the volume with large NTFS File Record Segment (FRS) (4096 bytes instead of 1024 by default) as you could face NTFS limitation errors in future. You could verify FRS size with the following command:fsutil fsinfo ntfsinfo <volume pathname>
Command to reformat NTFS volume with larger FRS (/L):format <volume pathname> /L
2) Use maximum NTFS allocation unit size(cluster size) of 64Kb.
Considering option mentioned in pt. 1, two commands should be united into one:format <volume pathname> /A:64K /L
3) Avoid growth of files more than 1TB;
4) For Backup jobs preferred backup method is Forward Incremental with Active Full backups enabled.
Introduction to Data Deduplication in Windows Server 2012: http://blogs.technet.com/b/filecab/archive/2012/05/21/introduction-to-data-deduplication-in-windows-server-2012.aspx
Plan to Deploy Data Deduplication: https://technet.microsoft.com/en-us/library/hh831700.aspx