Yes, you can transfer your scanned data from ScanSnap Organizer, CardMinder, and ScanSnap Receipt to ScanSnap Home during the installation of ScanSnap Home. Even after you have started using ScanSnap Home, you can still transfer data through ScanSnap Home.
For more information, refer to: ScanSnap Help (Migrating Files from an Existing Software Application to ScanSnap Home) 