place fot custom *.tpl.php files

Good question - here's how its done:

1) First copy/paste the node.tpl.php from the main Genesis theme to your Subthemes folder.

2) Then, copy it AGAIN, and then re-name it to node-story.tpl.php.

Now you have both node.tpl.php AND node-story.tpl.php in your Subthemes folder.

This is how Drupal template suggestions work, i.e. this is not a limitation of Genesis, its just the normal way Drupal works. The root template (such as node.tpl.php or page.tpl.php etc) must exist in the same folder as the template suggestions template (such as node-story.tpl.php or page-front.tpl.php etc).

Also - always clear the theme registry when adding new templates, Drupal wont see them until you do (Performance settings > Clear cache data).