Help a beginner - where to start with layers?

[Japhasca]

Layers are, essentially, layered graphics. They help when you want to display something above a previous graphic without removing that old graphic (they prioritize in viewing from top to bottom.)

They appear top to bottom, and layer's you've unclicked are invisible. They still exist, but if you save a file in a way that "flattens" the image, or "flatten" it purposefully, all VISIBLE data is scrunched down to one layer and anything unclicked (invisible) is thrown away.

A layer with less than 100% opacity (changed by double-clicking the layer and altering the transparency) affects the view of every layer beneath it by putting a recoloring affect above it (defined by the color per pixel and the transparency amount.)

If you want to create multiple variants of one image, you could use layers for that. Save a master copy in .pdn format. Then, open it repeatedly, change the layer settings, and save it how you want (do not overwrite the original file!)

You can alter the priority (what appears above what) in a layered image by clicking and dragging a layer in the layer window and moving it up or down.

 

As an example, I am making an RPG. I have some bookshelf graphics.

The basis is the outline (layer 1.)

I have a wood coloring (layer 2.)

I have a white paint coloring (layer 3.)

i have a "rotted wood" recolor done by using a semi-transparent layer with green pixels drawn over the normal graphic (layer 4)
This is my output files:
Regular wood: 1,2 visible, flattened.
Rotted wood: 1,2,4 visible, flattened.
White paint: 1,3 visible, flattened.