Many clients they may need to insert their own javascript or something else within the html head section of their pages. To do that you would not make changes within the following:

/main_page/header.tpl

The above template only contains the visual header that appears at the top of all pages within the default design. To add something to the html head you would do so within the html head of the follow page templates of the default design:

/main_page/basic_page.tpl
/main_page/category_page.tpl
/main_page/front_page.tpl

All the above are used within all "listing/category browsing" on the client side of the site. You'll find they are used in 99% of the pages visited by clients to your site. The following page templates are used within the client area and cart pages of the site:

/main_page/cart_page.tpl
/main_page/management_page.tpl

Basically for most configurations of the software the latter page templates only appear to those that are logged in. But in some "anonymous configurations" the cart_page.tpl could be viewed by those not logged into the site.