Correct me if I'm wrong, but basically, the way SEO (Search Engine Optimisation) works, is that either you (or your web designer) linked your home page to lots of differenent directory sites. This makes your homepage more "important" than competing sites who haven't done this, in the eyes of the search engines. In reality though, any good site will have done this, so this simply puts you on a level playing field.
However, within your own website, you could consider that the various pages are "competing" with each other. So the reason the homepage keeps popping up, and not the page you want directly linked to, is that the search engine views the homepage as the most important (which it is) because it has so many back links.
If you want to make individual pages important, you have to complete the same process with them - submitting them to lots of directories.
However, be aware that this may detract from people visiting your homepage, and I believe that first time visitors would probably like to go to a homepage first, and then be guided onto the next page.
You've done searches before where you get taken straight to a very indepth page, and you're not sure if you're in the right place, so you want to click "Back" to get to that sites homepage, but the Back function doesn't work because you were directed straight deep into a site, when you would rather have gone via the homepage. With me?