Sorry "Crabby Old Geezer" Dave, but I could not disagree with you more.
Layers are one of the best things that Trainz have introduced. Their one weakness (and this has been the subject of many a thread in these forums) is that there is no onscreen indication of which layer is currently open and active. This is most likely the cause of Jayco-man's misery.
To answer your question "What could they [layers] possibly be used for in Trainz anyhow?? You're working on a scene that is all one huge layer anyhow" ...
I use route layers to provide different options for the sessions I create based on the same layout. For example: A route layer containing trackworkers and their trackside machinery that would be present in daylight sessions but not in a night session, so I make it invisible in the night session. Other route layers allow me to temporarily hide assets, such as station buildings, that block my ability to place and move other nearby assets - such as seats, luggage, etc on the platform.
I use session layers to place the consists used in each session. I also use session layers for placing trackmarks and triggers that allows me to tailor the AI commands to each session instead of cluttering up the route with all the trackmarks and triggers. I also use session layers to show some assets, such as signalers operating levers when they are needed, and to hide them when they are not - all controlled by track triggers.
My best practice for dealing with layer issues is to lock all layers that you are not currently working in. An extra step I know but it will avoid the misery experienced by Jayco-man.
I really don't know how someone could create a complex layout or even a simple one with multiple sessions without using layers.
My opinion.