After you purchased the Unlimited Personal license and entered it in BoxCryptor on your PC, you can create a new BoxCryptor Folder with filename encryption enabled. Then you do the following on your iOS device:
1) Open the app and connect to your cloud storage provider (e.g. Dropbox)
2) Browse to the new BoxCryptor Folder you created on your PC
3) Enter the password
4) And voila, that's it. You can now encrypted and decrypt your files.