Site Sculptor does no apply the template to the index page so that the index page can have a unique look.
On the index page, i see the following left over template code at line 16:
<!-- TemplateBeginEditable name="head" --><!-- TemplateEndEditable -->
open the index page in a text editor like Text Pad to remove that code.
I see that there are quite a few HTML comments on the index page and in the template, these comments can through of the template engine sometimes.
to make edits to the sub page navigation, you should edit the template.
The index page has it's own menu, to make edits to the index page menu, you should edit the index page.