I save one master folder with the raw files in the root folder, then a folder for FLAC and a folder for MP3 (and a folder for project files, if I save the project).
That I back up onto an external as well as generally backing up the FLACs and MP3s to either/both of the LMA or the nyctaper server (if the recording appears there).
I am now in the process of making redundant external backups as well. I do keep one offsite, in my office, also.