Windows uses the following locations to determine which apps are started automatically on a given computer:
Folders:
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup
C:\Users\USERNAME\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup
Registry:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Run
BatchPatch does not contain functionality for directly manipulating these folders and registry values, but you could optionally write a custom script to do that, which you could then deploy to each target computer by using the ‘deploy’ feature in BatchPatch.