The only way I know to tell is to manually calculate the underpayment penalty and see if it agrees. The key is, does it apply an overpayment from the first column to the amount due in the third column. (If you don't have an overpayment in the first column it should correctly calculate your penalty, as far as I know.
So:
1) Did I have an overpayment in the first column (which is two quarters worth this year?) If not, things are good. If yes, then...
2) Did this overpayment apply to the amount due in the third column (in spite of the blank second column.) If yes, then the error is corrected. If no, then the error is still there.
Regarding the long method, you only need to use this is you had uneven income through the year. Uneven payments don't matter, and it neither eliminates nor exacerbates the error above.
