Stage 2 of the smart submission process simply allows the user to search selected areas of your site and then presents links with potential answers. Without the Smart Replies add-on enabled, the search uses the regular WordPress search engine.
Even though Stage 1 only allowed you to choose from three Post Types, Stage 2 allows you to search any Custom Post Type in your WordPress installation.
Configure this in the Stage 2 section in the TICKETS->SETTINGS->SMART SUBMIT tab.