While CLONEZILLA will image the drive, your ideas about imaging one or the other OS is going to enter a tar pit if you ever attempt to restore those areas. Rather than repeat all that's been written why not image the entire system?
This mess is a result and many folk but there is no one partition to backup for either OS and then if you restore one or the other SET OF PARTITIONS and they are not in the same order and even then neither will boot.
I fear that some feathers go well with this idea.
Bob
I currently dual boot Vista w/ Ubuntu. Soon I'll be dual booting Linux Ubuntu Natty w/ Windows 7 as I've just ordered a new machine w/ Win 7 pre-installed.
I've also ordered an external hard drive (2 TB) which I plan to use for images and backups.
I've never imaged before. And I'm none too proficient at backing up, either.
My new machine will have one single--1 TB hard drive. I plan to separate this hard drive into only 2 partitions, one for Windows and one for Linux.
Does my dual boot rig pose any special problems for saving images?
Will an image capture both operating systems?
Will I need to image each O.S. separately?
As to "ordinary backups", I'm pretty certain that I will need to backup each O.S. separately.
Is this correct?
And does anyone have any recommendations for an imaging program? Free is nice, but I'm ready to spend a few bucks for a more reliable program.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic