Midi Notes to Treble AND Bass Clefs.

You need to choose which staff to enter notes on. (Click a rest in Bass clef)

You can only enter notes on one staff at a time.

Realistically, notating music in such a way - all notes above middle C on top staff, all notes below on bottom - would seldom produce readable results. Real music is more subtle than that. Anyhow, you don't say how you are trying to enter the notes - which of the various MIDI note input methods you are using. In the default step -time, you need to enter notes left to right anyhow, so there is no getting around needing to enter the staves separately. You could if you want enter them all onto a single staff then right click and choose the "Split Staff" command to move notes to a new staff, although as I said, results would likely be not very readable as they would not make much musical sense. Or if you prefer real-time input, you could play into a sequencer, save as a MIDI file, then import it into MuseScore - using this method you will get somewhat more musically-sophisticated splitting of notes between hands. But in the end, there is no getting round the inherent impossibility in the task - MIDI simply doesn't present the sort of information needed to produce readable music automatically. One way or another, you are going to have to spend effort cleaning up the results to produce readable notation. Just as you'd never dictate an entire thesis into Siri and expect not to have to do a ton of cleanup.