Hmmmm, I'm not really sure since I usually merge it once I'm happy with how it looks like. I usually have the background, the line art in very low opacity, the silhouette of the main thing, and then a bunch of layers masked on top. I keep adding layers until I have to transform the entire thing which then I would merge them all :>

My process has become 'whatever feels faster' so I could no longer include step-by-steps because I usually just merge them all in the process (because it's the easiest way to manipulate the entire painting) ;w;

Althoooough, as I checked the .psd file, the final thing says layer 10...