On-the-fly encryption refers to concept of disk encryption. It means that data are automatically encrypted or decrypted right before they are loaded or saved, without any user interaction. No data stored on an encrypted volume (storage card) can be read (decrypted) without using the correct password.
The files are accessible immediately after providing the password, and the entire SecuBox volume is typically mounted as if it were another storage card of the mobile device. This makes the files as accessible as any unencrypted ones. You can do anything with SecuBox secure storage card that you can do with a normal Windows Mobile storage card; only that with this Windows Mobile program, the SecuBox volumes require password authentication before the protected data becomes accessible.
Files can be copied to and from a mounted SecuBox volume just like they are copied to/from any normal storage card. Whenever you save information to this encrypted Windows Mobile storage card, it is automatically encrypted. Whenever you read information from this Windows Mobile storage card, it is automatically decrypted. The entire process is transparent to you.