Custom Press Php insertion into the template file

Hi Guys-
I am new to WPMU, so bear with me, but I am trying to insert the php and shortcode into the custom single.php file.
I need to know where exactly to place it- as in, under the header, above the footer, etc... the guide wasn't specific enough for me. I placed the taxonomy php on line 10, right above the word header, and inside the loop. Is this correct? I have a bazillion taxonomies, and want to do it right the first time.
I can link a screenshot of my template file if that helps-