We too have HA configured. When I first got involved with Control-M two years ago, I did the manual service stops and server reboots as this is what I had been told we need to do. I have had this same conversation with BMC support and was told that we did not have to stop the services or reboot the servers in any special order. Our next patching cycle, I let it run automatically including the server restarts and all went well. The only thing I did was stop the services on our HA server since I did not want it to be primary. It patches in a later patching window. What we have since done is set up a Control-M job to stop the HA services prior to the automatic patching window and to put our servers in maintenance mode in our enterprise monitoring system (Zabbix). Now we do nothing for our automated patching that occurs Sunday morning. We have mostly safeguarded this window from having jobs scheduled in Control-M as this is our standard maintenance window for the majority of our systems.
Hope this helps.