This is one of my favorite things:
If you create a commentary (such as "My_Notes), you can link it to a widget in the Bible panel (File > Preferences > Bible & Verse Panels > Verse Widgets), then when you want to make a note, click on the widget and the commentary will pop up so you can add the note for that verse, or if you want to read a note you made previously, it will show in the 'preview' popup when you hover over the widget. If you want to add to the note later, Shift + click will open the entry in the editor. In the editor, if you want to enter a verse, you can type the reference, then Ctrl + t, and the verse text will fill in for you, then you can read the whole verse in the popup preview when you hover over the widget. You can, of course, always open your commentary in the commentary panel, just like any other commentary.