Internal linking is highly important. it allows the
PR to flow through the site and it also creates topical relevance for each page. I get the impression that you are focusing on the home page for the wrong reasons. It shouldnt always be the home page that appears for a search but rather the most relevant page from your site (which should be the one which you have tailored to that particular phrase). One of the ways to attach a page to a keyword is to link to it (from within and from outside of your site) using that keyword.
Do you catch my drift?