Although obviously sometimes using the literal subdomain to differentiate sites works, in many cases the user experience is more complex, with having multiple sites under the same subdomain.
In Chimera, the most direct way to do this is to define multiple sites in the the site group. In this way you can isolate your analysis at a particular site, and also there's a site field.
Sometimes you only realize there are what users consider sites once you are fairly deep in the analysis, originally approaching it in a more monolithic approach. If that's the case, you can use maps to derive sites (or potentially scrape it out).