When you mark out your rafters for a 2x4 wall, use 4" for the seat cut, as you don't want to have to notch your boxing around your rafters. Put the boxing up before you install your rafters, then put the plumb cut tight up against the boxing. This way your rafters sit across the entire 2x4. You want to make sure you brace the walls securely and make sure everything is straight and plumb before installing the boxing.