CPS Upgrade and Multiple Method Servers

I was doing a patch on my test server and ran across an issue where Windchill didn't start.  Ultimately I think it was because of not running the update_tool after completion but the error pointed me to this article... CS197660.  However, I only had one method server.  My question is, do you always have to reduce your method server to one when doing a CPS update or can I leave all the settings alone?  My test server cannot handle more than one method server for me to test this.