N.Y. Comp. Codes R. & Regs. tit. 20, § 2397.5
(3) Where a taxpayerparticipating in the program establishes to the satisfaction of thedepartment that it has made an overpayment of tax for a particularperiod by EFT or certified check, as applicable, the taxpayer shallclaim the overpayment as a credit on the return covering the periodfor which the overpayment was made. A taxpayer may call the taxpayercontact center or utilize the program's website for help in resolvingany questions involving credits.
(c) Special paymentrule.
Where a taxpayer required to participatein the program is liable for payments of taxes described in two ormore of subparagraphs (i), (ii), and (iii) of paragraph (1) of subdivision(a) of section 2397.2 of this Part, the taxpayer shall make separatepayment by EFT or certified check of the taxes described in each ofthose subparagraphs.
(a) Amount of payment.
On or before the applicable due date of each calendarmonth a taxpayer participating in the program which has liabilitydescribed in either subparagraph (i), (ii) or (iii) of paragraph (1)of subdivision (a) of section 2397.2 of this Part shall remit itsrequired payments of tax by EFT or certified check in accordance withthe provisions of subdivision (c) of section 10 of the Tax Law.
(b) Payment of remainingliabilities.