The 1040X should show the difference between the two so it sounds correct. Don't mail the1040X until you get the refund form your original return. Also, it may print showing Do Not File because it won't be ready to print until mid-February.
The amended return doesn't catch up to and replace your original return. The IRS processes them as two separate returns and it raises the possibility of confusion if you have two returns in the system at the same time. It takes the IRS 8-12 weeks to process an amended return.