Your preferred scan settings, image save destinations, and the applications you want to use are saved in the profiles.
You can scan documents simply by loading them in the ScanSnap, selecting a profile, then pressing the Scan button.
It is also possible to add new profiles and modify profile settings.
Note that profiles can only be used on the computer that they were created on. To use the same profile on another computer, export the profile on the computer that it was created on, then import it to the other computer.
To export/import profiles:
ScanSnap Help
(Select the model name of the ScanSnap at the top of the page)