We are using Avamar succesfully in our environment.
We use it to do our Full backups and we backup t-logs with native backups to the file system, then sweep those up with Avamar's Windows File system backup.
Yes, the databases take longer to back up due to the de-duplication I'm guessing, but since that overall saves us on storage I'm for it.
As far as copy-only, yes you can still take your back up with SSMS or script, and use copy-only.
Our backups are scheduled to start when it makes sense for our business, and they occur somewhere between the start time and the Avamar black out window start time.
*We dont back up dev and test unless our developers request it, and we have a separate data set for those environments.
We have separate data groups based on the retention, frequency, and exclusions for the database sets (i.e. SharePoint db servers do not need SQL backups if using the SharePoint plug-in so we exclude those). We also have some servers that need special settings so they are in their own data set.
Apparently (we have not tried this) you can Script your Avamar backup. This gives you total control over over how it executes on your db server, and you can run your integrity checks, etc. prior to the backup, probably along with your performance throttling if you so desire.
We have had backups time out due to ghosted Avamar processes (avtar.exe) on the database server because of multi-channel backups, but we catch that with our alerts and SQL policy checks, kill the processes that are ghosted, and re-run the backups.
We would like to see Avamar do a db integrity check before starting the job as part of the built-in options to the backups.
VMDK backups. The snapshot agent available with Avamar freezes the I/O on the vmdk, so to some applications this is problematic and we have had to discontinue automatic scheduling of these snapshots. Instead we use our NetVault snapshot agent and manually schedule maintenance windows to do Avmar vmdk snapshots.
*Note: I would not trust a vmdk snapshot to backup your database, it is not database transactionally aware.
Finally, I would like to know how to sync msdb with the actual backup files in Avamar so it knows when the backup files are gone. If anyone knows how to make this happen I would really appreciate a ping back.
Hope this helps, and if anyone knows how to sync msdb I'd really appreciate your comments!