To execute the reorganization, copy the generating CAB (reor.cab) in the model\bin directory to the device or emulator and execute it.
After that, execute the reorg.exe in the \program files\<installation directory>\ folder.
Note that the reorganization create the database. (See SQL Server CE Configuration )

To deploy the application, you only need to copy the bin folder to the device or emulator and the client.exe.config to the same folder.