I've used the EaseUS disk copy tool to mirror an old hard drive to a partition of identical size on a new drive: http://www.easeus.com/disk-copy/
It's pretty straightforward. You'll probably want to make sure to disconnect the old drive before you boot up or it could confuse Windows. You might need to assign the new drive (partition) the old drive's letter to keep everything working. I can't guarantee you that you won't run into some programs having trouble, but this worked perfectly for me with a boot drive the one time I did it.
So if you've got 2TB on your RAID 5 and you're cloning a 500GB drive to it, you'll end up with a 500GB partition on the 2TB drive and 1.5TB that you'll have to do something else with.