Because privacy is important to Google, we need to know you own a site before we'll show you certain information about it or enable you to use our tools (for example, to request indexing or removal of a URL). Verification doesn't affect PageRank or affect your site's performance in Google's search results.
To prove your ownership of a site, add it to Webmaster Tools and follow the steps to verify that you control the site. Add your site now.
Make sure you sign in to Webmaster Tools using the same Google Account you use for Custom Search.