Adding Google Custom Search

Would like to add google custom search to site, using this methodology:

http://digwp.com/2010/10/google-cust...o+WordPress%29

If I wanted to replace the default search and put Google CSE in the same location, where do I add search box code:
searchform.php
-or-
header.php
-or-
/functions/bfa_header_config.php