You can use macros %time%, %date% within directory names you want to synchronize.
Example:
Let's assume you have a directory "C:\Source" which you want to backup each day into a time-stamped target directory like "C:\Target_2009-10-08". All that needs to be done is setting up base directories like these:
Source
folder: "C:\Source"
Target
folder: "C:\Target_%date%"
Latter will be interactively replaced with the current date during synchronization. In order to further automate this process, you can create a *.ffs_batch file with this configuration and choose "ignore errors" to avoid the warning that target directory is not (yet) existing.