Adding PHP to my template for the WooTumblog theme

Like many others, I do great with installing the plugin on my website (www.nofactzone.net) until I get to the part where I need to add the PHP. Can you please give some advice as to how I can edit the field to add the PHP with my template? I do not have access to loop.php in my WP editor for my template, but I do have access to these PHP files:

* Comments
(comments.php)
* Main Index Template
(index.php)
* Theme Functions
(functions.php)
* chameleon.php
(chameleon.php)
* start.php
(start.php)

I was hoping that a simple insert to the functions.php file might work as that seemed to be the solution for another user. Thank you!