With my MIDI sequencer, you figure that out on your own. You drag rectangles around the hand's notes that are the easiest to pick out, and that'll move them to that other hand's track.
So, manually, you:
Figure out if the piece is even playable by a human - sometimes it's for a computer to play (a bunch of hugely complex, blisteringly fast arpeggios a human has no hope of playing).
Play through the song and see where your thumbs end up.
Edit the MIDI and pick out the notes that need to move.
You really can't do this in an automated fashion. There are too many variables (like hand span, fingering, hands hopping over each other, a finger on one hand poking in 2 notes, there's all kinds of craziness that can happen).
So, you get a piano player, and have him/her do it.
Your question kind of boils down to "how do you place your hands when playing a piano piece."
Answer: Learn to play the piano.