Improving search engine ranking position is never ending job since Google always change its algorithm to provide relevant search to its user.
To improve your search engine ranking position is to get inner links from each web pages from your site itself, you have to make sure that you built some good internal links from the existing pages this would help Search engine put some authority for the site and in turn will improve your search engine position.
Another way is to submit your inner pages to article directory is the easiest way to get incoming links for inner pages. By the way Internal linking is the best way I would suggest if you have not already and if you can categories sections of your website and make a content page for each category listing the pages within this category. That will increase the number of internal links.
Also if it's an article/informational website then on the home page always update your home page with your new latest articles and obviously add a link to them. Building a unique content so that people will link to you without having asked them to do. And, if you have a blog, social bookmarking sites are your best friend to get good quality links for deep page.
Deep linking is important since when the search engine are seriously searching for the quality sites. For me the best and easiest way to building your interlinking is started with a strong internal structure and internal linking architecture for the site's 1,000 pages. Group them by category/topic or whatever other relevant grouping you can find, and then after writing the content for those pages, link them together appropriately using the keywords I want to target in the links I'll be creating to not only enhance the user experience (by linking to relevant and related pages within the site) but also to improve the rankings in the search engines. These links would go in the CONTENT themselves, with relevant keywords and other search terms surrounding them (as needed and appropriate).
Then I'd identify the best of the best of those pages and start promoting them, working my way down to the other pages as needed once I have links for my "best" pages coming in from other sites.











