The Preferences Window

The preferences window give you the ability of affecting the behavior of File Synchronization.
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The first section gives you control of what File Synchronization will do in the case it encounters an error while performing the synchronization. You can just log the error and continue. After the synchronization is done, a list of errors will be displayed. You can stop the synchronization and display the error. You will then be given the choice to continue the synchronization or cancel it. The last choice will completely stop the synchronization. You will be presented with the error, but you won't be able to continue the synchronization.
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File Synchronization has also the ability of creating a log of what happened during a specific synchronization. You can see in that section where exactly will be saved the log. The format for the log filename will be YY.MM.DD-HH.MM.SS.txt. The log file will be created in your Library folder, in Application Support/File Synchronization. You also have the ability of opening the generated log file in the default application for opening text files.
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This section lets you choose what to do with deleted files. You can have them removed or erased by default, or if you enable the Move files to trash instead of deleting them, File Synchronization will do just that, move them to the trash. You'll be able to review the deleted files before it's too late. Note that due to a bug in the Finder, even with files that are moved to the trash, the trash icon in the Dock doesn't always shows that there are files in it. But if you click on the trash icon to open its window, the Dock/Finder will realize that files were thrown away and will change its appearance to a full trash can. The files will appear in the trash window. The other setting, Display an alert before deleting or moving an orphaned file to trash offers extra protection. If you enable this setting, everytime that File Synchronization is about to delete a file or move it to the trash, an alert dialog will appear and you will have the choice of continuing the synchronization and deleting the file or stop the synchronization altogether.
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This section gives you control over the repeated synchronization. If you set some pairs of folders or files in the main window for repeated synchronization, you can set the auto sync at launch and the repeating time interval in this tab.

The Automatically synchronize pairs that are selected for repeated synchronization when File Synchronization launches checkbox does exactly what it says: when launching File Synchronization, the pairs that have been set for a repeating synchronization will be synchronized. If you want to temporarily disable the auto sync at launch, immediately after launching File Synchronization, press and hold the Spacebar key when the main window appears and hold it down for a few seconds. The Automatically quit after synchronizing will quit File Synchronization when the last pair selected for repeated synchronization has been synchronized. If there are any error encountered, the synchronization will stop and you will have to intervene to fix the problem.

The Repeating Synchronization section lets you set the time interval used to repeat the synchronization. You have a choice of minutes, hours or days. Note that if an automatic synchronization is due to start and there is already a synchronization in progress, the automatic synchronization will be canceled for that specific time and will be repeated after the time interval. If any error are detected, the automatic synchronization will stop, waiting for you to fix the error. The time interval will start when you click the Close button. Note that pair set for an automatic synchronization will not be automatically synchronized at launch. Only the pairs set for a repeated synchronization will.
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Finally, the last section is called Interface. The checkbox Closing main window quits File Synchronization gives you the ability of quitting File Synchronization when you close the main window. The List row height slider lets you adjust the size of the rows in the table of the main window. When changing the size, you can have a preview below the slider of how the rows will look like.

The Mount remote volumes in background will let you continue to use File Synchronization if you click on a pair of folders that has one of its folder located on a remote volume. If you turn this option off, then each time you click on a pair using a folder on a remote volume, File Synchronization will block waiting for the system to mount the volume. That means you won't be able to perform an operation and File Synchronization will be totally non-responsive. This can take from a few seconds up to a minute if your network is slow or if the remote volume is attached to a slow computer. NOTE: this option should be turned OFF if you're planning to do any type of automatic synchronization. If you don't turn this off, when File Synchronization performs an automatic synchronization, it will try to access the folder on the remote volume and will not wait for the remote volume to mount. This will generate an error that will stop your automatic synchronization.

Finally, Show Growl Notifications will turn on or off the Growl notifications. Note that even if you have Growl installed and set to display notifications from File Synchronization, you will have to turn it on here to see them in Growl.
At the bottom of the window and always present are 3 buttons that will change their appearance depending on your actions. Initially, only the Close button will be enabled and the default button. If you make any change to any preference, the Revert and Save buttons will be enabled, with the Save button becoming the default button. Note that any change you make won't be active unless you save those changes and then close the preferences window. For example, the time interval for the repeated synchronization won't start until the window is closed.