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I doubt the command "dd" cares whether the partition is ext2, ext3, ntfs, vfat or whatever. It simply reads the disk directly and writes to another partition or to a file.
I have not used "dd" much for backup purposes, but I would make a large partition for the backup drive so that all other partitions can fit onto it. Then I'd instruct "dd" to write the other partitions to files on the large backup partition. This way you'd end up with neat files residing on the backup partition.
Otherwise you'd have to create lots of unneeded partitions.
Btw. "dd" copies the data, not the master boot record. You'll have to recreate it in case of a system failure.