To be honest, there really isn’t a whole lot you would need to do differently in terms of developing your own custom templates for the plugin. With all three of those files, WordPress will handle the loop, so the only thing you would need to worry about is presenting the content, the taxonomies and the metadata. For that, you can just look at the code in the plugin. There are some global hooks added by the plugin in /inc/func.php and you can look at how the shortcode handles displaying the information for ideas on how to present it differently in your theme.
