MIDI Feature Inputs

I wonder if it's possible for the MIDI to read left and right hands when you input them onto the score itself. Like, you won't have what you play over on keyboard be inputted onto the track itself as one bar instead of having both clef and treble inputs on the same section.

Don't know if that makes sense...

I've uploaded a file that makes clear of what I'm trying to convey.
MIDI Readability for both right/left hands when note inputting