An overpayment of tax on the 2019 return can be applied to 2020 quarterly estimated tax payments, but It will be applied as of July 15, 2020.
The Department extended the due date of the first quarter estimated payment, extension payment and the tax return from April 15, 2020 to July 15, 2020. The due date of the remaining quarterly estimated payments for 2020 did not changed. For example, the second quarterly payment was still due on June 15, 2020, and should have been made on that date regardless of any overpayment that may have been computed on the 2019 return.
More information: Important Notice # 20-05 Franchise and Excise Tax Notice COVID-19 Tax Filing Extension