In Joomla there is a sequential approach that needs to happen when setting up a Multi-Domain environment.

Of course, the first part is running down the extensions you need, testing them, learning them, implementing them.

The second part is a continuation of the first.  More specifically though, you want to build out your Array of Resources.  I would prefer this to be a checkbox rather than a Bullit List but here we go.

First Requirements

• Stable and Controlable, generally Linux based Server - lots to this but I can help.
• Joomla Up to Date - should be easy
• As many of your Extensions up to date - should be easy unless some subscriptions have expired - move on
• Disable or Remove unused Extensions -  Many things you can do under the "Manage" tab on the backend of Joomla

Add Specifically

• Virtual Domains
• Smart Search (buildin)
• OS Map (joomlashack)
• Other Mappers for testing
  • Aimy SiteMap is helpful.  JSitemap is helpful, XML Sitemap Pro - external, is helpful
    • turn them off when you are not using the extras and don't submit to Search engines unless you need a second one for some reason.  Lots to discuss there.
• OS Content (a great way to start your content buildout)
• OS Meta (a great way to be sure you have covered your bases)

Remove:  

• Search Modules

Add:

• Smart Search Categories for each Menu
• Smart Search Modules to each Menu
• Custom Module that links to each of your Virtual Domains
• Second Custom Module with Restricted Access for your in development Virtual Domains.
• You can also do this with Articles but I find it too slow
• SSL Certificate(s) for your domains (assumably applied in Apache)
• Google Analytics Code to each Template being used by a Domain, and segregated to that Domain
• Site Map registrations to google for each Domain  (you need to organize yourself here with Menus)

Test:

• You will test alot, so keep your initial structures as simple as possible
• Be Patient and Persistent.
• You should do the same tests on each of your domains sequentially.
• When all is working, move on to the next
• Keep a good Checklist for Issues.  You can even write notes to your system with restricted access

Know:

• You will get errors if you are repeating content in your menus the wrong way.
• That means,  do not include the same content in two different Menu Items exactly the same way.  One needs to take precedence.
• Move from one subject to the next throughly
• Joomla ACL is very powerful.  It is complicated.  It is useful.  It is not always obvious what changes, so test the differences in settings.  
• You generally won't kill your site, but sometimes you may need to remove something you just added that made your site stop working.
• Big Changes should be preceeded with a System Backup that you can restore from and which you know how to restore from
• I repeat:  Big Changes should be preceeded with a System Backup, manually triggered.
• Have a Daily Backup system in place as well.

Check:

• Your Virtual Domains Menu Filtering regularly.
  • If you add Menus Elements in Joomla you must add them to the "don't filter" (Menu Filter) set if you want to see them.
  • You can spend extended periods of time thinking your system is broken just because of this or some "bad key stroke sequence there.

Comment

• • An update to Virtual Domains was done recently, and it is clear that there can be more done.
  • All that said, it works very well and can save $ Time and Mind.  
  • Check out that Formatting Trick.  Never had 2 Bullets stacked before.
  • Have some fun and have some things to talk about other than your web site  (I am taking notes).