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To do multiple backups to a single drive you will need to either partition it (one partition for each backup, maybe another one if you really want to store other data on the drive, too), OR you will need to backup to sparse images on the drive itself.
I have not used the include exclude stuff much before, so I am not sure how you should set that up. Maybe "include <your folder>" followed by exclude "*". You could try things out by doing "backups" from one small disk image to another (so that SD does not have to scan your entire hard drive for each test run).
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