I have a lot of layers too. I tend to do the folders/organization a different way - by clicking on and selecting the layers I want grouped, then going to the drop-down menu at the upper right-hand corner of the Layers Palette and choosing New Group from Layers. Does the same thing!
I don’t see a way (yet) to lock a layer so that it can’t be moved from it’s place (order) in the Layer’s Palette. While I don’t really need this, it would be handy every now and then.
The other thing that had me annoyed was CC’s insistence on activating the “Shape Dynamics” box in the Brush Settings palette, which makes the line pointy at the ends and wider in the middle. I kept removing the “x” in the box and CC kept putting it back. As a result of our discussions on this topic I have explored further and finally figured out how to change its default and make it do what I want!
You’re right; in the layers palette are two padlocks. The black one locks the layer so you can’t change anything on it. The other padlock is to lock the transparent pixels in that layer.
I end up with LOTS o’ layers, so I usually group them in folders. (The ‘new folder’ is at the bottom of the layers palette.) You can put whatever layers you want into the folder, name it, and then lock the folder, which locks everything in it.
Does that help what you’re looking to do?
I had lots of teeth gnashing initially when I switched to CC, but there’s a lot I like about it.
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