If you don't already have a Webmaster Tools account, add your site to Google Webmaster Tools. Make sure to add and verify all your sites, including subdomains. You should do this using the same Google Account you use for Custom Search.
You can ask Google to crawl a specific page or Sitemap to discover links to other pages on the same domain. All new pages on the same domain as the specified page or Sitemap will be added to the index, and will be crawled and indexed. In addition, Google will periodically revisit this page or Sitemap to discover and crawl new links.
Request ongoing indexing of content linked from a hub page:
- On the Custom Search home page, click the search engine you want.
- Click Setup, and then click the Indexing tab.
- In the Index Now section, click URLs linked from a hub page.
- Click Add, and then type the URL containing links you want Google to discover.
- Click OK.
- Click Index now.
Each URL Google discovers and crawls in this way counts against your indexing quota. If you exceed your quota, Custom Search won't index discovered URLs until quota is freed up.