A 3 TB Fusion Drive works with Boot Camp. Mac OS X 10.8.3 included support for 3 TB hard disks, so you can use Boot Camp.
However, it's safer to use a virtual machine that will work without any problem. Note that Parallels, VMware Fusion and VirtualBox use a file as the virtual hard drive for the virtual machine, so you won't have any problem.
For most of users, a virtual machine is sufficient, but Boot Camp will give you a better performance because it uses all hardware
There are limitations with either choice you make.
With boot camp, that is where you partition the drive to install windows and have a dual boot system, and a fusion drive windows will be installed on the rotating standard drive only. Not utilizing the ssd flash storage at all.
If you go with a virtual machine install of windows in either parallels, vmware fusion or the free vm program virtualbox from oracle the limitation are in the virtual hardware used. Most specifically in the virtual video card all of the virtual machine program use. So if you are using graphic programs the preformance in a vm will be lower then if windows was in it own partition and using the real hardware in the system. On the plus side for a virtaul machine install of windows is that you can run both os x and windows at the same time, windows and the virtaul machine program might be placed on the ssd part of the fusion drive and will actuall run faster then if it was in its own partition on the standard rotating hard drive.
bootcamp require partition changes to the harddisk this caused problems with some version of bootcamp with fusion drives
virtual machines just make a big file on the normal harddisk you could even copy the file to an external harddisk and take it with you can start the virutal machine on another computer both windows and mac (not if it's parallel though because there is no version of that for windows but wmware and virtualbox have clients for windows)