Paying additional tax after filing a fedearl extention with payment.

Here's the deal, I filed an extension request thru Turbotax and paid the amount I thought would be owed. I've since found a stock sale I forgot about, and now owe more plus interest.

I'm getting ready to e-file, the software says it knows I paid the extra but when I'm about to hit enter, it tells me the IRS will take out the whole amount, not just the extra. That will bounce.  There's a place I can manually enter additional taxes already paid, but I'm not sure that's how to handle this. Help! The clock is running on the interest.

It's a software issue that I'm increasingly finding is a problem here.