No need or point in submitting any site to search engines; get links and they'll find you. Search engine results are for pages, not sites - so if your subsections are interesting, they can be found. Don't place key pages too deep, however, as they handicap them to some extent.
Few Quality Directores will list 'deeplinks', though if the topic really is totally different from the doamin.com, some may.
but if the content is quite different, why not go mad and buy a second domain? less risk of confusin, less risk of the 'deeper' pages not getting a fair go.