The encryption software creates a 'virtual encrypted storage card' on the smartphone. 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 the encrypted card - all you have to do is "unmount" the encrypted card - 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 is mounted and you are able to access the protected information on your smartphone. Without your password, the encrypted data on your Windows smartphone 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 work with the usual Windows Mobile storage, only that all information that you write there is transparently encrypted using the strongest algorithm acknowledged today - AES 256-bit.