UTSC now uses NSIS for installation, so just run the installer and follow the prompts.
When you run the application for the first time, it will create a Registry entry (less than a kilobyte) to store your settings.
The preset files (*.ut_pre) seen in UT Server Config 1.0 are no longer used, and neither is the "data\" subfolder. If you've written any, you'll have to convert them into new format datafiles (go to Datafile Creator on the main menu).
UTSC now includes an uninstaller, available via the Add & Remove Programs entry in Control Panel.
If you want to uninstall manually, you can run Regedit (c:\windows\regedit.exe on most systems) and delete the key "HKEY_CURRENT_USER\Software\pseudorandom.co.uk\Paradox Productions\UTSC".