Developing with PHPTemplate

I decided to migrate my site using the PHPTemplate engine. However, I am a PHP novice and have a
few general questions before I proceed.
As always with a new document I tried to deconstruct the box_grey theme and learn how it works. Here is what is not quite clear to me:

Do all the $xxx variables refer to stuff that is entered in the admin section such as the links content etc?

$head for instance seems to be set by using the set_html_head and get_html_head -I´m not sure how to do that. Can you call and set metatags that way?

What is the structure of the page.tpl.php? If you set primary and secondary links don´t they all have the url of the base url and the php takes care of customizing the head, title, and blocks for each individual link? Unfortunately I couldn´t really understand how the links work by box_grey. Some people also put count before their php link code. What´s the deal with that?

On top of everything else I have a rather complex nested table html design which probably cannot really be migrated perfectly. Even the navigation php code for the nav table will become a bit too challenging for a php newbie like myself I fear. Take a look if you want - www.playhigh.com

I´m greatful for any enlightnment you can give me.

Cheers!

Max