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In answer to the title question, make sure all your pages have at least two ways to be found via the crawling bot. If there is only one doorway in, it might be missed sometimes.
Make sure that all your pages link to many other nearby pages as well as your main pages.
See those links on this page "Home / Forums Index / The Search engine World / ...", those are called cookie crumbs. They are useful for both your users and for spiders. Use them if you can.
Once your links and your linking structure are straightened out, the best thing you can do is to get deep links to some of your content pages that are buried deeper in your site.
Googlebot follows links. If all the external links to your site point to the home page, whatever effort it puts into your site will always be through that one page. If you have several different entrances, it will find all the pages close to each of those entrances.
I recommend a tree-like structure where you can always get from the higher levels down to the more specific levels. Other structures work too, o' course, but when in doubt I'd go with a site map and a simple linking structure so that you can reach every page via the root page, or a page that the root page can reach.