There are various Link Modes that operate between windows.
For example, when you have an arrange window open and a score window in link mode, the score can either follow the folder level of the arrange window, or it can always show the contents of the selected track or region.
If link mode is off, the score window can be set to always show the full score, no matter what selection is made in arrange.
Those are just a few examples.
Read more detail in your manual....
Like Colin says, it is a way to have content reflected correctly between windows. I can have a region selected in the arrange window, and have the piano editor show the same region content, at the same location., If I select a new region, that one becomes the content of the piano roll. it works between editors of all types, so you could have a piano roll and an edit list all sync so you can see what data you want.
Just double click the link in the arrange (it turns yellow) and then the link in your edit window (it turns purple).
And yes, it is in the manual. Look at Apple for the complete manual, not the help type manual that opens when you hit help in the app.
Most excellent! Thanks for the answers, ideas, and links. Still need to pore over the manual some more. I actually printed the manual on a high speed printer. Forgot to turn on duplexing. Have a box beside me with 12" of manual. In color. 1 page per sheet. Dang me!!
Could not help notice the "Logic 9 TDM guide" among the pdf reference guides. Are any of the post 7.4 Pro Tools versions still compatible with Logic 9? I have been under the impression that TDM interactivity died with Logic 8.