Does Automatic Update in Patch Management automatically reboot the target machines? If so, is there a way to avoid this?
Check "Reboot Action" under Patch Management. That's what it does after patching.
^ Automatic Update is Step 1. You have to configure Reboot Action if you don't want users logging in with "your machine needs to reboot to complete the update" or whatever. You can try notifying user and let them cancel if in use, or just reboot at like 3 am...depending on your schedule.