In FMS 12 you can set the "keep x backup sets" number to 0, which will make FMS drop the backups directly into the chosen backup folder without creating a date/time stamped subfolder.
If you are on 11, do a google search for "backups, more backups!" for a white paper that I wrote some years ago. It comes with a VBscript and shell script that will do most of what you want. I will also be talking about this at Devcon.
Thanks, your answers are really helpful. I'll make sure to catch your session.