Links and Search Engine Ranking

[GVN]

Hi everyone,
I recently put up a new site. I included a directory for promoting the main site. I Put the directory in a sub folder /links/. After I got all this done I started to wonder about search engine ranking, in links, link popularity, and the like. I read somewhere it's important to have links pointing to the main page of your site for a better search engine ranking.
My question is.. Will the directory being in a sub folder and reciprocal links pointing to the directory and not the main site hinder it's search engine ranking?

Thanks in advance.
GVN