I dunno if it would be so farfetched that Kakashi was simply smart enough to figure out how to make the eye work w/ his body. It kinda reminds me of when Tsunade disabled Kabuto from using his body parts correctly. Kabuto, being a good ninja, quickly reconfigured what mental impulse controlled each body part and his body control was pretty much back to normal. Kakashi has had that eye for over 10 years now plus he's a genius. And we know that when he trains, he is extremely focused and sets high standards (ie climbing up a mountain one-handed). I dont think we'll get such an easy explanation that he simply figured it out but it might be along those lines.