Now, we're also looking to index more of your site's content for inclusion in your Custom Search Engine (CSE) used for search on your site. We figure out what sites and URLs are included in your CSE, and -- if you've provided Sitemaps for the relevant sites -- we use that information to create a more comprehensive experience for your site's visitors. You don't have to do anything specific, besides submitting a Sitemap (via Webmaster Tools) for your site if you haven't already done so. Note that this change will not result in more pages indexed on Google.com and your search rankings on Google.com won't change. However, you will be able to get much better results coverage in your CSE.
Custom Search is built on top of the Google index. This means that all pages that are available on Google.com are also available to your search engine. We're now maintaining a CSE-specific index in addition to the Google.com index for enhancing the performance of search on your site. If you submit a Sitemap, it's likely that we will crawl those pages and include them in the additional index we build.
In order for us to index these additional pages, our crawlers must be able to crawl them. Your Sitemap will also help us identify the URLs that are important. Please ensure you are not blocking us from crawling any pages you want indexed. Improved index coverage is not instantaneous, as it takes some time for the pages to be crawled and indexed.