I use carbon copy cloner for my hd backups. It makes an exact copy of my hd. I have a Bootcamp partition for my windows image. If I backup up my main Mac hd and it copies the image file from bootcamp does that mean that my windows hd is backed up too? Or do I need to make a separate backup of that too?
The best way is to use either low level disk copy tool as example only g4l from http://sourceforge.net/projects/g4l or special tools fro backing up windows partitions under boot camp for example winclone http://twocanoes.com/winclone/