adding toc in template file

Try the developer help notes under the help tab. This will give you the TOC index so you’ll still need to call the_content so it can add the anchors into the headings.

I hate to be that guy, but could you explain that a little further? In what order do I call the index and then call the_content? Is the toc content not showing up because I’m calling it before the_content? And is it the following code that gives me the actual toc:
echo '<ul id="my_toc">' . toc_get_index($content = '', $prefix_url = '') . '</ul>';

Ok I’ve got it to work using do_shortcode() but the only thing it prints on the pages is <!--TOC-->

Provided you are in the loop, you can retrieve the index with plainly $toc = toc_get_index();

You can then do whatever you want with $toc (change it, echo it, etc) but don’t forget the starting and closing ul tag. Seeing that you stored it in a variable, you can use it outside of the loop.

Later on, you’ll still need to call the_content() so it can output the content with all of the anchors.

Don’t use do_shortcode if it’s only outputting that.