If its filed before the due date, it will be processed like a superseded return...whats your concern?

I have a CA resident who worked in NY as a non-resident. Her CA taxes were $10000 and she paid $8000 in NY taxes. When I filed the original return it showed the balance due of $10000 because I had forgotten to put in the Schedule S for credit for taxes paid to NY. I filed an amended return yesterday which included the Schedule S for $8000 and the amended return shows a balance due of $2000. The amended return was accepted yesterday. I just want to be advised that the amended return will supersede the original return and so when client pays the $2000 there should be no problem. I am just concerned that the amended will act over the original return. I have never made such a mistake before and just want to be comforted that the amended will be what CA will consider when processing her returns.

The amended return will be the active one on CA files. The $2,000 is sufficient.  There is an incredibly small chance of CA sending a notice of tax due since the amended was filed ahead of the due date. If for some reason the amended is not in the client's account and a notice is received, a quick phone call will clear it up - the amended would have caught up by then. You did a great job solving the issue quickly.