You can choose the option to enable auto upgrade for an installation while installing it from Softaculous.
step 1: Choose the script you want to install. For this example we choose Wordpress.
step 2: Click on the Install tab and fill in the details.
step 3: Select the Auto Upgrade check box and then click on Install button.
That's it !! Auto Upgrade is now enabled for the installation you just made.
See the below screenshot to verify that Auto Upgrade is enabled for the installation.
If you forgot to check auto updates on intial intallation and want to enable it afterwards please follow the instructions in this kb article.
