It depends on why I'm putting on the insulation layer.
If it's a dry day, if I'm using my shell as a windshirt, and I'm wanting to add insulation on a break from hiking, I'd throw on the sweater/jacket/vest on over my shell. Why? It's faster and easier, and I don't want to get any of my sweat on my insulation, especially if it's down.
If I'm sitting around at camp and don't expect to take off the insulation, I'll wear my shell over my insulation, if anything to protect the insulation's delicate low denier shell fabric from twigs or ash.