Ha! You thought from that title that I was going to teach you how to document an app with 500 tables, 1500 TOs, and 2000 layouts? Nope. I'm as baffled as you are.
I read the discussion on What's the Biggest Monster of an App You've Made With Filemaker ? I suspect there are more than a few of us curious about how devs keep track of everything. Don't you occasionally look at, say, table occurrence #647 and think, "hmmm...why did I put this TO here?" How do you label or keep track of it all?
One small technique I use is to put comment boxes to the right of the relationship graph. With a (mostly) anchor-buoy structure, each buoy has a purpose noted in a comment box. That helps a lot, and I yet have a small fraction of some of the monster structures I see posted.
So tell us, ye monster slayers: how do you do it?