CPanel version 10.8.2.119 or later has setting the default /scripts/upcp to be run everyday regardless your Manual Update settings in WHM Config Update. The system will automatically send an email notification about this running cron to root user.
To setup this cron running time in WHM, you should have installed Pro and CronConfig modules from your WHM root account.
Login to your WHM using your root account. Go to CPanel section and click the AddOn Modules. Find the Pro and CronConfig modules and make sure you check the Install and Keep Update checkboxes.
Refresh your WHM after the required modules installed and go to the Add-Ons menu. Now you can enter the Configure CPanel Cron Times menu to setup the /scripts/upcp cron running time to any time period you want.