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Go to the download page, download the MSI file and run it. The installer will add a shortcut to your Startup folder.

You might want to check out the key binding for SCOTZ (on the 'General' tab) and the Recognised Apps tab.

Bring up SCOTZ by left-clicking the icon in the System Tray or use the key binding you selected (right-click on the SCOTZ icon and click 'Settings...'). Click the window you want to switch to. Alternatively, click anywhere in the application zone background. This will result in (a) a switch to the application window if only one window is associated with that application, (b) a switch to the window with the highest value (default is frecency, can be changed on the 'General' tab in the settings) if there is more than one window associated with that application or (c) the application being launched if no windows are currently associated with it. The behaviour associated with clicking the zone background can be changed on the 'General' tab in the settings.
You can also use SCOTZ to close windows by holding down Ctrl and Right-clicking the window you want to close. This same method can be used to quickly remove unwanted application zones.

'Auto-Detect' uses blacklisting: every application you ever use will be shown in SCOTZ except the ones you exclude. This means that you'll probably have to blacklist applications every now and then, such as installers. Alternatively, you can set SCOTZ to remove applications that have been unused for a certain period of time.
'Manual' uses whitelisting: only the applications you specifiy will be shown in SCOTZ. This means you probably have to add new applications manually every now and then.

Spiral, Squarified and Grid are options for the layout of the application zones. Spiral, as the name suggests, lays out your application zones in a spiral, starting in the top-left corner and heading to the right. Squarified order your application zones by frequency, from the top-left to the bottom-right. Grid simply uses, well, a grid. If you want to read more about squarified and spiral treemaps, we recommend the following papers:
Bruls, M., Huizing, K., van Wijk, J. (2000). Squarified Treemaps. Proc. Eurographics and IEEE TCVG Symposium on Visualization, pp. 33-42 (PDF )
Tu, Y., Shen, H. (2007). Visualizing Changes of Hierarchical Data Using Treemaps. IEEE Trans. on Visualization and Computer Graphics 13(6), pp. 1286-1293 (PDF )

By default, they are ordered by frecency, which is combination of frequency and recency. The item with the highest score is in the top left corner of the zone. Clicking anywhere in the zone, but not on a specific window thumbnail, will switch to the window with the highest score. Window thumbnail ordering can be changed to frequency of recency in the menu.

Alt-Tab uses the same ordering as "normal" Alt-Tab, which can be a bit confusing indeed. We recommended just pressing Alt-Tab once if you want to go back-and-forth between two windows quickly, but use the mouse to select a window in other cases.

Yes, SCOTZ includes logging. As SCOTZ is a research tool, we'd like to know more about how people use it. Only the makers of SCOTZ have access to the log files and we will never give your data to anyone else. However, your data may be used in publications about SCOTZ, though, of course, anonymity will be preserved. Once we have collected enough data a logging-free version of SCOTZ will be released. Also, if you feel uncomfortable about sharing too much information, you can disable logging of window titles in the settings, on the 'General' tab.

Go to the 'Advanced' tab in the settings and check the box. Change 'Morph' (bottom-right) to 'every 10 (or 15) minutes' instead of 'instantly'. Optionally, disable some of the fancy effects in the top-left corner.

Go to the 'Advanced' tab in the settings and check the box.