You know what would be neat 
If you could hover next to a verse Number and a Pencil show up. Clicking on this could bring up a text section under the verse for you to type your thoughts. When done the text stays there for you This could be removed from Visualization with a Bible Text Only feature for the notes part, maybe right under the Bible Text Only Option in the drop down menu, and it could be titled "Bible Text Only (Remove Notes)"
This is per Neil Ross' Post @ http://community.logos.com/forums/t/34387.aspx
