Calling the theme()-function in the page.tpl.php

Hello,

does anybody know how the theme()-function works in a page.tpl.php??
I can't figure out how to place other blocks within my sourcecode.
I customized the internet center theme a bit
and I found the following function call pretty confusing:

print theme('links', $primary_links);

because I placed my menuitems within a different block than primary links.
How is that possible or how can I add other blocks to my page?

Sorry but I am still learning ...

Thanks so much,
Soezkan