Best Arrangement and Definition of Layers

To add to other posters - treat layers as 3rd dimension - they are for your convenience to keep objects of the same kind / functionality in order.

Willi's points are all good ones. If you are going to use layers in multiple projects, keeping names identical will be a big time saver. Order, as long as you observe the purpose of each, is not as important since it's the work of a few seconds to drag layers to different order. Locking all layers that don't need changes is another very useful trick. (Ideally, only the layer you are actively changing should be unlocked, but that can get a bit restrictive. But things like backgrounds, guidelines, fixed elements... keep them locked so you don't inadvertently modify or select them.)

As for templates... don't put too much faith in their being some kind of absolute or perfect model. Few are as well-designed or optimized as they should be, and you quite often find quirks, if not flat-out flaws, in the way they implement layout and design features. Feel free to modify anything you dislike, and move layers around, and modify styles... as long as you understand that the reasons not to have more to do with "breaking" the layout than violating some arbitrary rules.

The most important thing is that the layers in all documents have the same name and the same order. It si important:

1. When you copy and paste (Paste remembers layers is active) InDesign remembers the name, not the order. If the order is different, Objects get a different orxer and can mess up contents.
2. When you move a page from a document to another, layers shuffle around and make a mess.
3. In Export to PDF from a book file, Acrobat recognizes the layers by name, not by order.
4. Even if layers are not used, they cost no space, do not delete them.

There are layers which have to be on top, like page numbers, runing headesrs, logo, so they are not covered by any content.

Other layers have to be always in the background, like background, so that a backgroun image or color does not cover other objects.

Other layers can be decided o or so, there are reasons to to soe and different opinions not right or false per se.

That is whatever the original designer felt was appropriate.