JD Builder is built with flexibility in mind and gives you complete control over the layout of your elements, not only via backend but with the ability to override the php layout files as well. Just like the core Joomla overrides.
All your elements are located in
ROOT/plugins/system/jdbuilder/elements/elementname/tmpl/default.php
To override the layout of this element you could copy the file over to.
ROOT/templates/yourcurrenttemplate/elements/elementname/tmpl/default.php
The upside of using overrides is that your layout files don’t get overwritten whenever JD Builder is updated.