I have a daily snapshot and understand that the snapshots are incremental, and would only take a snapshot of the difference from the last backup.
So if I take a manual snapshot, would it know to diff from my last automated snapshot? Or does it only know to diff manual snapshots?
The way snapshot works are:
It won't be differentiating between an automated backup or a Manual backup. It checks the existing backup (either a Manual or Automated one) and adds the delta on top of it. 
.If you have deleted the First backup, then the Second backup becomes the point of reference and it creates a soft link with reference to it.
