There would be an add, delete, and mark as done button for Notes in the editor, including a side tab with all your notes time-stamped and in chronological order. On the side tab, you would be able to click a note, and it would jump to that point on the timeline to see the place in the song that is being referenced.
When scrolling through the timeline, the notes would appear in the top left corner of the grid.
The notes would be represented as purple ticks on the hit objects timeline in order to distinct themselves from the rest of the marks.
Modding
For this to work:
A "Post to Forum" button in the Upload Beatmap tab would allow modders to leave notes in a beatmap, click the "Post to Forum" button, and then a hyperlink with their mod would be posted to the map's forum. From the forum, the beatmap creator could click the hyperlink, and their beatmap with all the notes marked on the timeline in the editor would be there. In order to organize each modder's notes, the side tab would have folders labeled with the modders name, in which you could click to display that modder's notes on the beatmap.
This isn't a completely necessary feature, but I think it would make modding and editing beatmaps more clean, organized and accessible.