One of the fields in the Google Search Appliance forms is "sitesearch". If you put a domain name in there, like this:
<input type="hidden" name="sitesearch" value="www.sce.cornell.edu" />
then only results from this domain will be listed. If you further qualify the domain with a subsection of the site line this:
<input type="hidden" name="sitesearch" value="www.sce.cornell.edu/ss" />
then only results from that section of the site will be returned (recursive search of subfolders). Add a trailing slash like this:
<input type="hidden" name="sitesearch" value="www.sce.cornell.edu/ss/" />
and results will be limited to pages in that specific directory.