Hi Darren,
The OU or Organizational Unit that you specify during the Installation Wizard will contain the Microsoft Dynamics CRM Security Groups, not the Microsoft Dynamics CRM Servers.
Keep in mind that Organizational Units helps you organize objects in the Active Directory. That being said, I would definitely recommend that you leverage the Organizational Unit structure that you already have to store the CRM Security Groups. Selecting
a specified Organizational Unit will help you locate your objects into the Directory way more easily.
So, the Organizational Unit that you will select during the installation will contain 4 CRM security groups:
• PrivUserGroup
• PrivReportingGroup
• ReportingGroup
• SQLAccessGroup
The Organizational Unit that you will specify during the installation will not affect the ability to add servers to your deployment later on. Also you can put your Microsoft Dynamics CRM Server objects inside different Organizational Units within the Active
Directory, this will have no impact considering you don't have restrictive Group Policies applied to those Organizational Units.
Make sure The user account used to run Microsoft Dynamics CRM Server Setup has organization and security group creation permission in Active Directory on that Organizational Unit. (http://technet.microsoft.com/en-us/library/hh699825.aspx)
For more information on OUs: http://technet.microsoft.com/en-us/library/cc758565(v=ws.10).aspx
And for more information on the Microsoft Dynamics CRM, please refer to the Implementation Guide : http://www.microsoft.com/en-us/download/details.aspx?id=3621
Sorry for the amount of information here. Please feel free to ask clarifications.
Hope this helps.