How to create custom markup in Moodle theme settings?

I need to create a list of elements in a Moodle 2.x theme setting for which I will enable drag and drop re-ordering using Moodle's included YUI. My problem is that I don't know how to add my custom HTML/JS with a custom theme setting. I can only find documentation about adding settings with the pre-defined functions offered by Moodle, like <code>admin_setting_configtext</code> or <code>admin_setting_configselect</code> or <code>admin_setting_configtextarea</code> etc... How do I go about creating my own markup and use my own javascript in a theme setting page? Thanks!