Yes, you only need to update the CurrentControlSet key…
ControlSet001 and ControlSet002 are alternating backups of
CurrentControlSet, you don’t need to update them.
Edit: As K noted, CurrentControlSet is an alternating symbolic link to either
ControlSet001 or ControlSet002. The other key is kept as a backup for the
Load Last Known Good Configuration boot option.
Edit 2: See Microsoft KB Article 100010: What are Control Sets? What is CurrentControlSet?
Original page link broken, see archive.org backup page instead.