What's the difference between the MSS and MSRT?
They serve somewhat different purposes. The Microsoft Safety Scanner will review your computer on-demand for any viruses or malware. The MSRT is specifically targeted at a small number of malware (specifically common botnets), and is not designed as much to be run manually. Instead, the MSRT is designed primarily for its monthly Windows Update releases, after which it will automatically scan your computer in the background (If you have Windows Update enabled, the MSRT is running once a month without you knowing). So, the MSRT is an attempt to stop botnets without the user having to take any action, while the MSS is a simple tool for concerned users that will check for everything Microsoft knows about.
You can open MSRT by typing in MRT into a Run command box, this will open a GUI for MSRT, click the "View a list..." link, here you can see a list of the narrow target range of the tool. This list is occasionally updated through Windows Update, when the list is updated it will silently run the tool in the background looking for new threats. Logs for MRT are stored in C:\Windows\Debug\mrt.log