I open WHM, go to Plugings and open - Softaculous - Instant Installs
Softaculous opens in a new window, there I go to Software - General Scripts and select Freescout (the script I want) - there I check the 'Install' checkmark and press on the 'update settings' button on top of the page. Then it showed it was updating the files and that the settings where changes successfully.
After that I go back to WHM, and search for 'Freescout' - but it does not show up at Plugins.
In order to install the script you need to login as cPanel user.
So from WHM you can go to "List Accounts" select the account in which you want to install the script and click on the "cPanel" icon next to that account.