After you install all of the Nuke_Cron files, there should be an icon for Nuke_Cron in the PHP-Nuke admininstration panel; click on it.
Click on the New Cron Job link, enter a brief description of the job so you can identify it in your saved jobs list, enter the server path to the script (or the path to the script relative to your php-nuke installation), enter a time increment for the job to run, and click the save icon.
The new job will execute as your website receives traffic at or around the time increment you set. The script you execute with Nuke_Cron will run in the background and will be unnoticed by your website visitors.
Ideally, the script you're executing with Nuke_Cron would be written in php, asp, or another similar language.
For example, Nuke_Cron could be used to initiate database updates, database backups, or anything else that requires periodic or continuous maintenance.
Good luck!