You can't upgrade the ATL-SCL flight on DL metal with CO miles, even though it is a CO codeshare. I'm pretty sure that the same holds for NW, but not 100% certain. Any fare other than full Y costs the 2x miles to upgrade; only Y fares are the 1x rate.
If you book the flight on nwa.com you have the option to add your CO OnePass number during the booking process; that part is pretty seamless.
If you actually want to be able to upgrade all the way to SCL you'll need to fly on Copa via PTY. You can connect in LAX or IAH and then on to PTY then SCL. Of course, the PTY-SCL flight is on a 73G with domestic F type seats/service, not the DL BusinessElite service/seat.