unfortunately this is quite tricky at the moment.
The feature to encrypt already existent files in your cloud via Boxcryptor for mobile devices is on our road map, but I can't name an exact date on this.
You could either use the Boxcryptor Client for desktop systems or Boxcryptor Portable to encrypt these files.
Boxcryptor portable may be downloaded here:
To encrypt the file with Boxcryptor for mobile devices, you would need to open the file with Boxcryptor. You may select the file within your DropBox app and send it to Boxcryptor.
Afterwards there will be two files on your DropBox. The encrypted and the plain file.
Just delete the plain file afterwards in your DropBox.
Hope this helps.