I am running an ISP. Many of our clients want Web hosting along with their own email addresses. When setting up Exchange on one server that is hosting multiple FQDN, the domain that is set up first becomes everyone's e-mail address. For example, if I set up mysite.com as the primary domain name, everyone that I am hosting (theirsite.com, hissite.com, hersite.com) has an email address that reverts back to mysite.com.
How do I give each client their own domain name e-mail address?
Perhaps I'm misunderstanding your question, but on the e-mail addresses tab of each mailbox you can specify the SMTP address that the mailbox will use. You can set that to be any address for any domain that is pointed at your Exchange Server.