Thanks for posting Johnstone. Can you be more specific? What seems to have disapeared? Give me as much detail as possible and I'll check it out for you.
Another important difference between the two is that uploads via the web interface do not track future changes to the files on the computer; whereas auto backup uploads via folders chosen in the PC/Mac client do.
Which of those is more suitable will depend on how you are using the coud. In particular be aware that if you delete a file/folder from your PC/Mac, it will be deleted from any auto 'backup' made via the client interface. BT Cloud is not a proper backup solution, it does not remember history for modified or deleted files. You can probably recover accidentally deleted files from Trash; but that is only available from the web interface, does not remember the folder structure, and therefore is not usually suitable for recovery of more than a few files.