Display Custom Post Type in Custom Taxonomy URL

You can use WordPress’ ability to accept custom rewrite rules to get this done. You can add the following to your functions file, or create a plugin (recommended).

function url_rewrites_wpanswers() {
    add_rewrite_rule('/custom-post-type-slug/([^/]*)?$','index.php?post_type=custom-post-type-name&custom-taxonomy-name=$matches[1]', 'top'); //lets you use /posttype/customtaxterm
}
add_action('init','url_rewrites_wpanswers');

You would have to add a line for each since otherwise yoursite.com/something1/something2 would end up pointing to:

yoursite.com/index.php?post_type=something1&custom-taxonomy-name=something2

Keep in mind, with the functionality that you are requesting there can be conflicts with your permalinks if they are set to /post-type/post-name

You can read and learn more here: http://codex.wordpress.org/Rewrite_API/add_rewrite_rule