The most obvious way would be to use 2 client resources like ...

the file backup client ... 
  Save Set:                   All-NTFS
  Backup Command:      savepnpc

the VSS backup client ... 
  Save Set:                   VSS....
  Backup Command:      save -a "ignore-all-missing-system-files=yes"

What do you think?

+----------------------------------------------------------------------
|This was sent by carsten_reinfeld AT avus-cr DOT de via Backup Central.
|Forward SPAM to abuse AT backupcentral DOT com.
+----------------------------------------------------------------------