Yes you first need to fill out your return like it was originally filed. Then save your return. Then when you hit the Amend button the refund monitors at the top should reset to zero before you make your changes.
The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.
You will have to print and mail the Amended return.
