Hi Adam,
Thanks for choosing IntellyWP products.
Unfortunately this feature is not still available from the settings of our plugin
If you want customize the timer and hide the seconds field in the countdown timer, you need to edit the following file:
/wp-content/plugins/intelly-countdown/includes/classes/ui/CountdownUi.php
and remove, at line 94 and 95, the following php code:
$this->drawSeparator($countdown);
$this->drawDigit($countdown, $countdown->labelsSeconds);
Let me know if you have any additional questions and will be a pleasure to help you.
Cheers
IntellyWP