You can use the "startHistoryManagement" method to enable browser history management for the Custom Search Element.

startHistoryManagement is documented in the Custom Search Element JavaScript Reference.  (In the "CustomSearchControl Methods" section, find startHistoryManagement about half-way down the page.)
http://code.google.com/apis/customsearch/docs/js/cselement-reference.html

Here is a demo.  View the source code to see how the startHistoryManagement method is used.
http://googlecustomsearch.appspot.com/element/history/

-- omr