Operating the ScanHelper application is quite easy, but requires a few steps to set it up
- Download the ScanHelper application which can be found here.
- Unzip the archive and copy/move ScanHelper to /Applications
- Open System Preferences->Accounts->Login Items and add ScanHelper to this so that it starts up each time you login.
- Double click the ScanHelper icon. You will see a small icon in the menubar.

- Click the ScanHelper icon and choose Configure. .
- A dialog will appear like the following (When you first launch ScanHelper, the configure window will be blank)

- Drag in applications that accept PDFs and you'd like to use as "helper applications" for your ScanSnap. For instance, drag in ReceiptWallet, DocumentWallet, Preview, etc.
- Launch the Fujitsu ScanSnap Manager Software
- Make sure the Quick Menu option is unchecked if it is available
- Select Settings. Click on the Application tab.
- Click Add or Remove. Then click Add. Then click Browse and select the location of the ScanHelper application. Click OK.
- Enter "ScanHelper" under application name. Click OK. Click Close.
- Make sure ScanHelper is selected in the popup menu.
- When you want to change the scan destination, click on the ScanHelper icon in the menubar and select the application.

- Simply press the Scan button on the scanner and your scan will appear in the right application
While this may seem a bit convoluted, once you get it setup, things work smoothly. This type of functionality should have been built into the ScanSnap Manager software as a dock menu, but it wasn't as Fujitsu probably didn't expect people to be switching applications all that often.