By default, Webtrends tracks visitors across the primary domain and all sub-domains. This is done by setting a first party cookie on your primary domain with the leading dot, which allows sub-domains to also read this cookie.
The values stored in Webtrends' first party cookie are used for maintaining session and user identification across all your sub-domains. If you need to track your sub-domains independently, then you can use the fpcdom config settings. The default name for Webtrends' first party cookie is WT_FPC, but you can change the name by using the fpc configuration setting.
For cross domain tracking, Webtrends uses a third party cookie set to the domain of your collection server to track users across your domains. For example, if you wanted to track users between myDomain.com and myDomain.net, you couldn't do it using only a first party cookie.