Agree that you should be aware that the VFAT filesystem (for example, /MyDocs and /media/mmc1 which is the microSD card) does not store permissions.

But having said this, when backing up to VFAT all that happens is that a few errors get generated: rsync complains "I couldn't change the permissions", but the files themselves are backed up. If you replace the "-a" with "-rt", then the warnings go away. ("-a" is short for "-prtlgoD", if I recall correctly, so you're taking away the "-plgoD" part.)

The problem comes if you try to restore, and you need those permissions. Not such a big deal with backing up "/home/user/", but if you try to restore, say, "/bin" and the permissions are screwed up, then so are you. Another reason I just back up the home directory and let the system restore take care of the other directories.

Don't let the permissions/filesystems thing keep you from doing frequent backups to microSD. Better to have files backed up with wrong permissions than not to have a backup at all. You could do a rsync backup to microSD a few times a day, and at least have a safety net in case you delete some data file.