All of the cPanel updates seem to run at exactly the same time on all VPS accounts, is there an easy way to fix this so its not maxing out the cpu at the exact time, besides editing the cron job for the upcp?
You may Install an Addon Module named cronconfig that let you set the cron time for upcp and cpbackup cron job time.
After installation, reload the WHM left menu and you will find "Configure cPanel Cron Times" at the Add-on section on WHM.
BTW: We have using cpanel for 3 years updating cpanel automatic daily with no issues. But it's allways your call