You can update ad group negative sites along with your placements when you use the Make multiple changes tool.
If your list includes both positives and negatives, the tool will add or remove them as you specify. However, it isn't possible to update campaign-level and ad group-level negatives at the same time using the Make multiple changes tool.
There are two ways to distinguish negatives from positives.
Option 1: Include a Type column, and specify Negative for each negative site. (You don't need to explicitly specify positive placements, because positive is the default.) Here's a sample list:
positiveExample.com
negativeExample.com, Negative
negativeExample2.com, Negative
Option 2: Use a minus sign (-) to designate negative sites. Here's a sample list:
positiveExample.com
-negativeExample.com
-negativeExample2.com