I don't know about anyone else, but I like to use the markup tools when I'm studying, marking the important words and phrases (in Bibles and Commentaries) - so I use the Highlighting pane frequently. In fact I like leaving the Highlighting pane open for quick access.
But one thing that bothers me a little is the fact that the Highlighting pane takes up screen real estate whenever it's open.
So, I would like to suggest that Logos add the option to auto-hide the Highlighting pane. If implemented it would allow a user to leave it open and yet it wouldn't take up space from the rest of the layout - it would pop-out over the top of the current layout and disappear again when finished.