TwoCanoes, the developer of Winclone, has posted detailed instructions on the procedure which makes the Windows partition be the fourth partition within the first 2.2TB of the drive.
In order to make Windows bootable on a 3 TB (or larger) drive, the Windows partition must be the last of the first four, and be contained within the first 2.2 TB of the drive. Disk Utility makes this easy to do. Shrink the existing Macintosh HD partition, and create a DOS partition so that if you add up the first four partition, they will be less than 2.2 TB total. The EFI partition and recovery partition are small (together they are less than 1 GB). Do not partition right up to the 2.2 TB limit, but leave some space. A good rule of thumb is that the Mac and Windows partitions added together should be less than 2 TB total. Finally, create a Mac partition that uses the remaining space following the Windows partition. Note that this partition will not be accessbile by Windows, but OS X will be able to see and use this space.
You can find their posted instructions at the link below.
Read More [via 9to5Mac]