Hi Trent!
I’m not sure if you are refferring to the search form on the results page: http://i.imgur.com/IkhHZPr.png
If yes, then I’ve looked at the theme code, and there was a tiny mistake there, as they accidentally hard-coded the search form to the template, so Ajax Search Pro was not able to override it. I’ve corrected the mistake in the theme file, now if a search form is selected on the ajax search pro settings, it will override that search as expected.
The file I have corrected is: \wp-content\themes\jupiter\views\templates\wp-search.php
You can make a back-up copy of it just in case.