In Wordsearch 12 I used the Create a new document to make outlines that had Scripture references that were hyper links that would go to the Scripture in the Bible running in the parallel Window when hovered with the mouse cursor. Can I do that in Logos or will the reference just pop-up the small text hover window?
Yes, if you have a reference in notes, it creates a hyperlink that will open in your main Bible. If your Bible is already open in parallel it will open in that window.
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To clarify, you actually have to click the link, otherwise it just hovers in the popup.