Unfortunately, the documentation is silent on this matter and when I was trying to discuss this issue with the support, I was advised to setup 4 different GMC servers. Since this sounded as serious overhead for my needs, I decided to look into it and try to find more convenient path.
Let's suppose you have the following situation (like I did):
- 4 email domains (domain1.com, domain2.com, domain3.com and domain4.com)
- User's accounts with multiple primary email addresses (i.e. some have their primary email set to email@example.com and others as user@domain2 or user@domain3 etc)
- Single Microsoft Exchange 2003-2010 organization with several mailbox servers
- Google Message Security (Postini) as your mail gateway (GMC's prerequisite)
- Google Apps domain (another GMC's prerequisite)
First question you'll ask yourself, is what domain name you should use for Google Apps. From what I found, it doesn't really matters.. I chose the domain which had the most users set as primary email address but in reality it not that matters.
After your Google Apps domain will be provisioned by Google (the registration process for GMC require you to sign-up for Google Apps Standard domain and afterwords Google will 'upgrade' your account to have necessary features for GMC) you'll need to add additional domains to it.
Login to your Google Apps account via http://www.google.com/a/domain1.com (replace domain1.com to your real domain name which you have used to sign-up for Google Apps).
Go to 'Domain Settings', then 'Domain Names' and click on 'Add a domain or a domain alias'. Make sure you chose 'Add another domain' (and not 'Add a domain alias') and put your additional domains name (one-by-one).
You'll need to verify these domains using various methods Google offers. After successful verification you will be able to provision your users in Google Apps.
Usually, I am using GADS (Google Apps Directory Sync) which I did in this case as well. The result of this will be user accounts created in Google Apps according to their primary email address (such as firstname.lastname@example.org, email@example.com, firstname.lastname@example.org etc). It's important not to forget to sync also user's aliases (proxyAddresses attribute in Active Directory) so you users will have all their aliases available in Google Apps as well.
Another catch is that GMC is only capable to work with a one Exchange Server. In my case, I had a single Microsoft Exchange 2010 organization with multiple mailbox servers within it. I found that if I configure GMC Server to work with one of them (doesn't really matter which one) it will be able successfully open mailboxes on other Exchange servers and retrieve the necessary data from there.
If your Microsoft Exchange environment consists of more than one organization, I guess you're out of luck and then the only workaround is to really install several instances of GMC Server. One more option which you can research is to use Application Virtualization. While I never tried it myself with GMC, tools such as VMware ThinApp or Spoon Studio should be able to package GMC Server and allow several instances to run on the same physical (or virtual) machine.