You can call the number on the 8879 and get the duplicates for June/Sept/Jan canceled, its too late to get the double April one canceled though, so you may want to cancel everything that you scheduled, adjust the next 3 quarters for the double payment in April, and schedule the updated amounts on IRS Direct Pay.

Oh and when you call to cancel, make sure you tell the rep that they were EFILE payments, not EFTPS!  One that I tried to cancel last year the lady told me she didnt see anything scheduled, she was only looking at EFTPS, so I didnt get it canceled whooo my client was so pissed when June and Sept pulled double, I had to prepare her return pro bono this year due to my F up!