A backup or raid system with ntfs partition without losing my data?

Hey guys we have a newb to linux here :) Right, here's my senario, I "had" a 3tb external hdd formatted to ntfs which I have lots of my dvds ripped on and was connected to a media center PC. I also have a 2tb WD MyBook World network drive with lots of important files on it that I have collected for years (ie. photos, family videos etc...) which has started having problems. I also have a 1tb WD MyBook World Edition which has failed. I decided to build my own overkill NAS, I purchased a nice case (Hoojum Cubit) a nice mainboard and another 3tb drive exactly the same as my other. I took the drives out of their external cases and put them in my new NAS box and I run my ubuntu 11.04 from usb stick. I have already setup samba and mediatomb, installed webmin and got it sharing the files/folders I want. but the hdd with all my files on is still ntfs. So my question is what's the best way to mirror my hdd with the one I just purchased?

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