HyperV & SQL
For the SQL Server (on Hyper-V), I'd probably schedule regular full/diff, and T-Log backups in SQL Server to a local drive that will then be backed up with the Hyper-V VM by CloudBerry. I cannot comment about the time clock software that uses SQL Server. Likely that company has backup guidelines for their software - and may be running backups automatically in the background. Since it's not a SQL Server database you likely have to manage on your own, it's best to follow the product's recommended backup instructions. If you do manage the SQL Server, though, then you can just back it up as needed and let CloudBerry sweep up those backups as described above to the cloud (or wherever you send your backups). If you run your own SQL Server backups outside of CloudBerry, you'll need to manage retention on those files - meaning, delete the backups when no longer needed locally.
If you want CloudBerry to manage the SQL Server backups (and retention) separately from Hyper-V VM backups, you would have to use a the SQL Server version and install it in the VM. It may be easier since we can manage the backups, scheduling, and retention - all without having to use a lot of local disk.