In VSTS 2010, silent installation has been added to Controller and Agent setup.
Run setup.exe /full /q from command line.
The configuration can be done through UI or command line tools.
To configure through UI, go to Start->Programs->Microsoft Visual Studio 2010-> Microsoft Visual Studio Test Controller 2010 Configuration Tool for controller configuration; and go to go to Start->Programs->Microsoft Visual Studio 2010-> Microsoft Visual Studio Test Agent 2010 Configuration Tool for agent configuration.
To configure through command line tools, use TestControllerConfig.exe/TestAgentConfig.exe under D:\Program Files (or x86 on 64-bit machine) \Microsoft Visual Studio 10.0\Common7\IDE. Type /? for helps.