The encryption software creates a 'virtual encrypted storage card' on the PDA. Data encryption happens automatically: files are encrypted on-the-fly when they are written to the encrypted card, and decrypted when read from the encrypted card. When you have finished work with SecuBox encrypted card - all you have to do is "unmount" it - it will then become a single file - a complete mess of characters which would take hundreds of years to bruteforce.
Whenever you mount the storage on your Windows Mobile device, SecuBox asks you for your password. Once you enter the password, the secure storage card is mounted and you are able to access the encrypted data on your PDA. Without the password, the sensitive data on your Pocket PC is completely inaccessible to any malicious user or anyone who wants to get access to this data.
You can write files to this encrypted storage the same way as you would do with the usual Windows Mobile storage card, only that all information that you write there is transparently encrypted using the strongest algorithm acknowledged today - AES 256-bit.