I think I misunderstood your question.
If you click within the pane where you want to take notes, it will make that pane active. Opening a new or existing note within that active pane is as easy as clicking on an already existing note from the explorer or creating a new note using the button above the explore or pressing ctrl+n.
One trick that I find helpful once I have established a complex folder hierarchy and I want to create a new note within a certain folder, is to open a note that is already in that folder first, and then creating a new note.