If you're concerns are page ranking, I would suggest that you do quality link building don't rely on the index page that will take care for your rankings it will be more helpful if you do these SEO techniques such as article submission, blog commenting, blog hosting, directory submission ETC. hope this helps.

whats the correct way to do linkbuilding? if for example i am doing directory submissions, the URL will be my_sitename/pagename.php. what about the link name and description?

In SEO, this is known as the "deep linking ratio" and is the percentage of your links that go to your home page and the number of links that point to other "internal" pages.

The bigger your site, the higher the percentage of links should go to your internal pages. The fewer pages your site has, the higher percentage of links should go to the home page.

For a very general rule of thumb, if you have a site with 50 pages or less, have about 50-70% of you links point to the home page, the rest spread over the rest of your pages.

If you have a site with 1000 pages or more, shoot for 60-80% of the links to point to internal links.

But your own site link structure is important too...If you have 1000 pages on a site, which 20-50 are your MONEY pages? The ones getting traffic? Use your own site pages to focus links on your money pages.

Think of each links as a little flash light, which pages do you want them all to shine their lights on?