Is it possible to have all links from the passage guide go to "one" window instead of opening multiple windows? You know like logos 3. In Logos 4 too many windows open!!
Unfortunately you cannot control this completely. What I have found is that if you have a passage guide open you can open say a commentary in one panel; a lexicon in another; and say an encyclopedia in another. When you open another commentary it should open in the panel you have a commentary open in. Same is true with the lexicon or encyclopedia.
I would suggest utilizing the saved layout feature to create productive workspaces that meet your needs.
http://wiki.logos.com/Layouts__
http://vimeo.com/17254785
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