Configuring Controlled Substances in SETWorks
Is there a way to make it so that Schedule II medications require a witness signature?
Yes, there is a setting that can make it so that if a medication is marked as a "controlled substance" in the medication utility then it will require a witness signature.
This is controlled by the following privilege:
Settings > Provider Build > Maintain Privileges > Consumer Profile - Health:

"Require the pin of a second staff member to administer controlled medications"
Once the privilege has been activated, navigate to the Medication utility and set the medication as a Controlled Substance:
Now that the medication and privilege has been activated, set up a scheduled medication in the consumer profile.
Observe that the controlled substance will require the PIN from the staff administering the medication as well as a second staff person who acts as a witness.