I represent AfterLogic support team.
Main question here is: are all those domains hosted by the same mail server? Current edition of WebMail Lite is designed to work with a single IMAP/SMTP mail host, so if you'd like to access multiple email hosts, I'm afraid it's not going to work with WebMail Lite - at least, not without deep tweaking. You might consider using the Pro version instead.
But if this is actually the case of all the domains hosted by the same mail server, you simply need to supply its host details in default domain settings, and any user on that mail server should be able to log in, regardless of the domain.
While there's no guaranteed free support for Lite version, you're welcome to post your questions at community forum: http://www.afterlogic.com/forum/forum_topics.asp?FID=21