Hi,
if you compare you either could do this with the frontmost windows or you could ( in case you use a treeview) select which document is left and which right. I both cases you end up with a side by side comparison of the two selected documents and in the bottom a third window that states the differences per line. Here the first line in that window is selected and so also the first difference in both compared documents.If you klick in that third window on the second lien, the focus of comparison will change to the next difference and will highlight it. there is no special setup to do so.
My quick tip with bbdiff means you need to have the cmd-lines tools installed ( This is under the BBEdit Menu a point). When you have done that you could open a Terminal and start the diff with bbdiff <first file> <second file> and you will see again bbedit with the three windows like descripted above.