Time Machine Strategy?
If you have a 3tb drive would you not partition it? 1tb would be HUGE for OS and apps, I can't imagine the number of apps you'd need to fill that much space. Do remember though, that you'd still need to backup your data (SuperDuper and Carbon Copy Cloner are sometimes more useful for data backup). As you have a MacPro then dropping a new, smaller boot drive in should be very simple and then you could use your 3tb drive just for data (iTunes etc). You might also think of a smallish ssd as a main boot drive (even 128gb is probably fine for all the OS and Apps you'd throw at it). This would boot very fast and apps also load a lot faster.