3 source drives -> 1 dest drive -> 3 destination folders
 

I have three removable drives that I would like to back up to three subdirectories on a file-system built on a single large HW raid partition. The reason is so that I don't have to manage destination partition sizes and I will be able to use any remaining space as a "scratch" drive.

I seem only to be able to map source drives to WHOLE destination drives (or partitions).

I can use sparse disk images on the destination drive, but even w/o compression there's overhead...for example I get 20 MB/s with FW 800 on a disk to disk backup, but less than 9 MB/s from disk to sparse image (source and destination devices also FW 800).

So is there any way to specify a destination as a subdirectory on a file-system (instead of the whole drive/partition) and still be able to use smart updates (to the destination file-system sub-folder)?

...and maybe the file-system overhead will be similar to the sparse image overhead, but I'd still like to try.

Sorry, no. You'd have to use sparse images to accomplish this.