I didn't create the mockup complicated enough to use the layers but for a real pixel-perfect design they are a must, in particular the ability to show/hide them individually. However, they would probably overcomplicate this product, I'd keep it simple.

Re: shift. When I press an arrow key, the object moves a pixel or two. If I need to move it 100px to the left, I have to either wait a bit or press the button too many times. If the step was changed to 10 or 20px if shift is held down, it'd be easier to move objects.