Mostly, when I've discussed pixel layers in this context, I've concentrated on cloning. But pixel edits can take many forms:
- noise reduction
- head swaps or other photo merges
- perspective correction
- skin smoothing
Perspective correction can sometimes be done in raw. Do it there if you can, but don't worry if you can't, because you can do it with wonderful precision in Photoshop.
The critical thing you need to understand about pixel editing is that each layer hides the previous one, thereby preventing it from being readjusted later. So it's vital that each step is perfect before moving to the next one. Let's examine a hypothetical nightmare photo that needs all five types of pixel editing.