I would suggest that making a cross-reference resource from the study bibles would be helpful. e.g. I have Ryrie's study bible. I wish I could make use of the extensive cross-references in that hard-copy bible in Logos.
Also, there are many charts and maps throughout the study bible which would be easier to find if there were a table of charts and maps which could be used to find helpful charts rather than scrolling through the whole reference work.