There is no "proper" way to do this, the drip rail "gutter" is the pinchweld that holds the edge of the roof together with the supporting structure. It's not just decoration.
However, If you really have your heart set on doing this, you'll want to do a few inches at a time, leaving most of the rail in place as support. Make sure your weld bead completely attaches all of the layers, or it'll crack, and give you structural problems.