I have a sub-directory that contains only a few pages. For SEO purposes, should I have a link from the index page of the sub-directory to the index page of the main site and visa-versa? Also, on the other pages within the sub-directory, should they also have a link to the index page of the main site or just to the index page of the sub-directory?
Every page on your site should have a link to the home page, just for good navigation. It would make sense for there to be a link on the home page to each section of the site, unless they were too numerous. Most on page SEO does not compete with common sense navigation and site design, IMHO.