@Zac, the shortcodes work on wordpress post or page not on template files. So you need to call the PHP appropriate PHP file to create the Add to Cart button. Have a look at the available PHP function in the PHP function references list:
http://www.tipsandtricks-hq.com/ecommerce/wp-content/uploads/2009/09/wp-estore-shortcodes.pdf
Or you can use the do_shortcode() function and pass the shortcode through it.