It appears there are two ways to specify an OU when joining a VM to the domain using a Guest OS Profile. The first is to use the Get-SCGuestOSProfile and Set-SCGuestOSProfile PowerShell cmdlets to modify the DomainJoinOrganizationalUnit setting used to join the domain. This is the most straight forward approach but is not visible in the GUI and is a bit more difficult to setup.
The second is to add an unattend.xml file to your VMM Library that includes the the MachineObjectOU element. In my case I used the following to join a 2012 Server to the "My Servers" OU on our Child.Parent.com domain:
<?xml version="1.0" encoding="utf-8"?>
<component name="Microsoft-Windows-UnattendedJoin" processorArchitecture="amd64" publicKeyToken="31bf3856ad364e35" language="neutral" versionScope="nonSxS" xmlns:wcm="http://schemas.microsoft.com/WMIConfig/2002/State">
The unattend.xml file will be merged with the settings provided in the Guest OS profile (like the domain join credentials), so this option will also let you customize other installation settings and will still visible in the GUI.