Under Windows, the Webinator install directory is stored in the registry. So there can only be one installed version of Webinator, as all versions will look for their config files in the same place indicated by the registry.
However, even though you can't have completely independent versions, you can use the same Webinator version on multiple sites (on the same host). Install it once, then copy texis.exe from the installed scripts dir to the new one, and also copy the entire wwwroot/webinator directory to the new wwwroot/webinator. You'll need to use different profiles for the different sites, if you want them to be different. Also, all sites will have access to all profiles, since there's still only one install.