I could be wrong, but I *THINK* for a 1120-S all you do is prepare the return as it should be and check the amended box.

If it was a 1040, then this is what you do, but I don't think this applies to a 1120-S:

1. Prepare the return exactly as originally filed.
2. Check the box to amend and check the year (and any state amended box as well).
3. Make the changes.
4. File by mail.