Layers is the primary reason I bought PSE10, but as I hate and despise the whole Photoshop interface I really try to avoid going there. I'm sure it's not Photoshop's fault, but to my mind, which is usually quite intelligent, I simply cannot get to grips with making layers, selections and masks work for me. I've done the tutorials and it just never sticks. Whenever I come to have another go it's back to square one on the learning curve for me.
As for files, maybe I'm missing a trick, but in Lightroom I have a raw file and my finished JPEG, if/when I choose to export it. I can revisit the file at any time and I never have the clutter of heavyweight intermediate files to be saved/stored. Indeed I don't need to save anything, or worry about which format I choose to save in. My impression of Photoshop is that once I'm done editing a raw file I have to save my edits in some cumbersome, humungous file, like a PSD or TIFF, if I ever think I might want to go back and rework the file at all. Well I don't want my drive cluttered up with both the raw original and some juicy, fat, intermediate file. I like the way Lightroom works. No surplus. No waste. All the adjustments there in front of my eyes. No concerns about 8 bit or 16 bit or flattening or merging or picking one file format over another.
Like I said, maybe I've missed a trick, perhaps several.