Both cores are contained in a single chip, so the object is to cool the chip. Tying to the hotter of the two cores assures that core won't overheat because the other core is cooler. On the computer I have that uses Macs Fan Control that is how I set it up.
I don't know if Mac Fan Control acknowledges one fan for the CPU and one for the GPU, but if so, then, yes, I would set it up separately.
SMC Fan Control is essentially the same as iStat Menues.
Personally, the internal fan control contained in the SMC chip in your computer is adequate to assure that the CPU and GPU do not overheat. I wouldn't recommend using any such software and trust that the Apple engineers know what they are doing. Laptops run hot because they are small, thin, and light. There isn't much room inside to provide huge cooling devices. Apple's manuals tell you not to use them on your lap because of the possibility of burning your thighs or causing overheating damage to the computer. Apple does not even refer to them as "laptops." They are called "Notebook" computers.
They also are not gaming machines. Although you can play some games on them any game that makes heavy demands on the processors will cause them to become uncomfortably hot unless you take external cooling precautions.