Currently, the only way to move files that are already on the server, is by downloading them and then re-uploading them to a different folder. This makes it very difficult and impractical to keep the various files organized. It's also difficult to download multiple files at once.
It would be very helpful if we could simply select any number of files and then click a "move to folder" button, that allows us to move those files to another folder. Alternatively, a cut/paste function would work as well.
As an alternative, I think you can look at using an option like FileZilla (free!). You can connect it to your BB FTP folder, and manage your files much easier. Plus, it doesn't time out like BB does!