Usually you use the URL builder tool when you have external campaigns like advertising on another sites, sharing links on social media, etc. It's normal that your advertisers will give you the destination URL with the tracking parameters they want so they can monitor their performance in GA on their end.
In order to track clicks on the banners you host on your site you should use either virtual pageviews or event tracking:
Classic GA: https://developers.google.com/analytics/devguides/collection/gajs/asyncMigrationExamples#VirtualPageviews https://developers.google.com/analytics/devguides/collection/gajs/asyncMigrationExamples#EventTracking
Universal Analytics: https://developers.google.com/analytics/devguides/collection/upgrade/reference/gajs-analyticsjs#virtual-pageviews https://developers.google.com/analytics/devguides/collection/analyticsjs/events
You can add a small delay so GA has enough time to execute the code.