If you want to monitor your IPv6 enabled sites or servers, simply tick the Use IPv6 box when creating or editing a check.
Inside the Add Uptime Check page, navigate to Web tab > Optional > tick Use IPv6.
One thing to keep in mind is that this will NOT monitor IPv4, so if you want to monitor both for a specific server or URL you'll have to set up two separate checks.
Also if you haven't done so already, allow all our IP-addresses access to get effective monitoring.
When the APM Integrated Experience is enabled, Pingdom shares a common navigation and enhanced feature set with the other integrated experiences' products. How you navigate Pingdom and access its features may vary from these instructions. For more information, go to the APM Integrated Experience documentation.