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Google Tracking and 3rd party search tools

We track our website using Google Analytics and just added a third-party search to our site (Endeca from Thanx media) they host our internal site search via a subdomain (search.highcountrygardens.com). Google Analytics lnow lists search.highcountrygardens.com as a referring site and it is throwing off our stats on # of visitors which then impacts our conversion rates by inflating the number of visitors to the site.  We used to have SLI as a 3rd party and they set it up so this was not an issue. Does anyone know how we can track subdomains (no matter where they are hosted) as part of our website and master domain?
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No explanation of how to roll together with filters