In the latest version of AjaxSearch (see here: http://modxcms.com/forums/index.php/topic,11228.0.html) This will be included in 0.9.6 also. There is a file named templates.inc.php that allows you to customize all parts of the output. When I added this I hadn’t thought of a site using multiple templates so it just includes this file. So for now to use 2 seperate templates you would need to create 2 versions of the snippet and then change the include paths in the snippet and in the file AjaxSearch.php
Not really the easiest thing to do, so I will look and see if there is a better way to do this.