Having trouble making custom textures with multiple layers.
So, I'm trying to make some custom textures with more than one layer. I add another layer to the texture in Paint.NET, save it, and then exit. Later I decided to open Paint.NET to modify the texture a bit, but when I loaded the file there was only one layer.
So, how do I make it so both layers save?
No standard image format supports multiple layers. Sorry.
Paint.NET, Gimp, Fireworks, and Photoshop all have custom ways to save textures with layers. I'm not sure what the Paint.NET one is called, but it should be the first option in the Save As dialog.
This.
If you want to save your multi-layer image to any format like .PNG, .JPG, etc., Paint.Net will warn you the layers will be flattened (turned into just one).
But I'm sure you mean a multi-layer .VTF file. In this case, Paint.Net will not ask or warn anything, it will just save your image, but it will still only save one layer, the sum of all the layers you had. This is not the right way to make your multi-layer .VTF files. If this is what you are trying to do (to later use the env_texturetoggle entity to switch amongst them) you need to:
1. Save each of your drawings under a different file name followed by an order number, making each image number be the layer number you want in the .VTF file. For example:
- my_texture01
- my_texture02
- my_texture03
2. Open VTFEdit and go to File > Import, and select all your different images. You can check that you imported all of your images correctly by using Frame +/- buttons, or even Play to watch all of your layers be displayed in a row in a loop.
3. Save the file under your final desired name.
useful tools and stuff here on TWP 
[spoiler]
[/spoiler]Having used Paint.NET now, the multi-layer format you want is called .PDN (for Paint Dot Net).
By the way, does anyone know how to open PDN files in Photoshop? I don't want to have to export each layer separately and import them one by one.