A single web server is often used to host many individual websites through a process known as virtual servers. An ISP will almost always divide the resulting entries in the main logfile into individual logfiles for each distinct website, so each customer's logfile contains only requests for its website.
If you host your own servers, you might generate a logfile that contains requests for all the subdomains of different sites, and you want to see these distinctly from each other. Your logfile contains a field that specifies the domain name of the site to which the request was directed. Logfiles in this format are known as multi-domain or multi-home. If this field is present, ClickTracks will compare the value against the site names specified in the New Dataset Wizard. The comparison matches, in turn, the domain names from the wizard, both the main site name and the alternate names. Lines from the log are discarded if they originated from a server not listed.
If the logfile is multi-domain and does not contain the virtual server name field then ClickTracks has no way to determine in which domain the request belongs. For Apache this field is the virtual server name or %v in the log directive line; for IIS it's cs-host. See Configuring Web Servers.
If your site has a number of subdomains that you'd like to analyze separately, make a new dataset for each and set the alternate server names such that only the matching names are included. Then import the same single logfile into each dataset.