Your company has a Windows Server 2003 Active Directory domain.
A server named Server1 runs Windows Server 2008 R2.
The Remote Desktop Services server role is installed on Server1.
A server named Server2 runs Windows Server 2003.
The TS Licensing role service is installed on Server2.
You need to configure the Remote Desktop Services Per User Client Access License (RD Per User CAL) tracking and reporting to work on both Server1 and Server2.
What should you do?

A.
Rename Server1 to have the same computer name as the domain and join it to a workgroup.

B.
Add Server1 to the servers managed by the Windows Server 2003 TS Licensing service.

C.
Uninstall the TS Licensing role service on Server2 and install Remote Desktop Licensing role service on Server1. Configure RD Per User CAL tracking and reporting on Server1.

D.
Activate the TS Licensing Server on Server 2.

Explanation:
Q: We have a Windows 2003 domain network and are planning to add a Windows 2008 R2 member server to the domain and use it as a remote desktop server. My question is this a supported configuration? If yes, should I install the TS licensing server on our 2003 DC and add the Windows 2008 R2 CALs in there or we should install the RD license service role in the same server as the Remote Desktop service role computer.
A: That scenario is supported. However, 2008 R2 RDS CALs can ONLY be issued by a Windows 2008 R2 Licensing Server. So yes, you will have to install the licensing role onto your r2 server and use that as the license manager.
Q: So all I need is to install all the necessary RDS components including the license services onto the member server and add the TS CALs in there. There is nothing I have to do on the existing Windows CALs license server or DC, right?
A: That’s correct. You will, however, most likely have to manually point your 2008 R2 RDSHS to the R2 license server (itself in your case).
Source: http://social.technet.microsoft.com/Forums/en-US/windowsserver2008r2rds/thread/561828c7-e7b5-4f9c-bae1-2331214a0ed7