Layer order in AE is doing my head in.

You'll want to learn the key board shortcuts for duplicating, arranging, nudging, trimming, and extending Layers.  Once you have those down, you'll have no trouble duplicating 50 or more layers and sending them up and down the Layer Stack.  After Effects shares shortcuts for arranging Layers with Photoshop and Illustrator, but I find it helpful to switch over to the ones that are unique to After Effects.

In addition to the keyboard shortcuts for selecting layers, using Labels is very helpful.

It's also possible to naviagte time via Layer shortcuts.

Let's say we want to select Layer 45 to 94, duplicate them, and then arrange those toward the back of the Layer Stack such that they're in front of Layer 120.  Select Layer 45 then press shift down arrow to add Layer 94 to add Layers 46 through 94 to the selection.  Then press command D to duplicate.  Change the Label color and then press command option up arrow to send them up and into a continuous stack and then command option down arrow until they're arranged above Layer 120.  It's easier to practice this with a small number of layers selected, unless you happen to the Timline panel on a vertical display with a high resolution.

A quick way to find all of the keyboard shortcuts is to copy and paste them to a text editor form the Visual Keyboard Shortcut Editor.

Also, don't forget that we can Pre-Compose Layers (effectively the same as Grouping in Photoshop).

-Warren

If you "duplicate" a layer, it goes above the second layer. Now there are 2 layers. One that isn't a duplicate and one that is. It would make sense that the one that isn't a duplicate would come BEFORE the duplicate.

+ AE tends to make layers bottom up (1 at the bottom, 100 at the top). Most of the time layers are sequentially placed to fit like that.