For defragging sake it is best not to mix your data with your system disk. Windows update followed by a defrag can take a long time if you have 0.5T of data. As noted, best to have multiple disks - but a system disk does not need to very big so what to do with that massive system physical disk.
One problem of the windows partition (Win 7 anyway) is that it cannot move data. If you have restore point turned on then the default position of the restore points is a very annoying place when you want to do a partition. You have to turn off restore point so that these restore files get deleted before you can shrink the disk by any significant amount; then turn on the restore and recovery mechanism. I have had to do this every time before partitioning a system disk disk. Unfotunately this article does not cover whether these tools manage this.
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