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. In addition to using the Google index, a CSE maintains its own index, striving to make sure that at least 10,000 pages from each site are available to return as results for your CSE.
If you're interested in letting your users search over pages that aren't currently being indexed in Google.com, you can let us know about these pages by submitting a Sitemap through Webmaster Tools. Any pages in your Sitemap that aren't included in the Google index will be detected and indexed for your search engine.
In order for us to index these additional pages, our crawlers must be able to access them. Submitting a Sitemap can help us discover additional pages on your site, and also lets us know which URLs are important. Also, make sure you're not blocking us from crawling any pages you want indexed with a robots.txt file or meta tags.
Improved index coverage is not instantaneous as it takes some time for the pages to be crawled and indexed. Please note that this improved indexing only affects search results within the search engine you create, not your rank and indexing on Google.com.