90% of the time, it is easier to recreate the old 1040 with all the mistakes, tax reported, credit reported and the whole enchilada. Then you save it. After that you invoke the amend return command and a copy of that return will be kept intact and a new amended file will be created. On the new file, form 1040 will stay and 1040X will be added. Work on the 1040 and prepare it correctly as it should have been done in the first place. After you review the 1040 and you feel satisfied with it, go to 1040X and enter the explanation of what happened. The calculations should be OK but take a look at the 1040X just to make sure. The other entries are easy to be answered with a check mark or entering a 1 on the correct column.
Going to your question, since 1040Xs are mailed and take a long time to process and some times we amend a year o two later, you will be better off if you roll over the old, incorrect 1040 file. The only time I think I will roll over the "amended" file will be if depreciation is involved. For example if they didn't include rental income for the 3 months (Oct, Nov, Dec) and I entered the cost and life of the house. Keep in mind that any required, extra form or schedule needed on the corrected 1040 needs to be attached to the 1040X. Also any schedule or form that change figures, needs to be included. For example, additional child tax credit form that had an entry of $250 and now has been bumped up to $760.
I said that 90% of the time it is a good idea to recreate the old, messed up return because:
Most 1040Xs report an extra W-2, 1099 series form, deductions not taken, dependents not claimed, credits not claimed, income not reported and errors by tax preparers. All these type of omissions are beautifully handled by the software if you follow what I said above.