Now when I do a search on Alltheweb, using url.host:[mysitehere]. It only shows my index.html, the one that I submitted.
Is Alltheweb going to spider my website at a later point? Or do I have to manually add each page on my site?
You can increase your site's importance to the FAST crawler by getting links from other important sites in your industry. The more connections you have, the more link paths a spider will have into your site.