Mac Pros with separate HDDs don't really need any magic for the "Boot Camp link".
Which Windows is it? Is your dedicated HDD formatted GPT or MBR?
For a one-time upgrade, I'd recommend you take a look at Acronis True Image with Plus Pack. They don't officially support Macs, but as long as you run it under Windows and include the Plus Pack to support GPT it should work well.
If cost is an issue and you want to try something cheap, you might want to give clonezilla a look-see.
http://clonezilla.org/ It has been a while since I used it myself, but it could work fine for your application.
B