A good piece of software that allows you to copy the entire partition and keep everything in tact is Partition Manager. http://www.partition-manager.com/
It's not free but it is worth it for the time you can save by simply copying everything at once.
You could also try some of these. I haven't tested them but since they clone while the OS is running it shouldn't have an issue with raid arrays. They are free so it might be worth it to try them first.
Another program on the list I'm looking at is PING. http://ping.windowsdream.com/
It sounds interesting but it won't work for RAID arrays because it's not going to be able to load drivers. Just throwing it out there for anyone else who reads this thread.