Right, I understand that you cannot use Expert and Config WebUI at the same time. I am not using Expert mode, and have used the WebUI exclusively. But what I was trying to do (as I was understanding it) was making edits manually to the file itself and uploading it via FTP to customize the files.
And what they're telling me is that custom edits to any configuration files that are then uploaded, have to be done while in Expert mode otherwise they'll be overwritten ...? Maybe there's a miscommunication somewhere or I explained it poorly to them. I don't know.