When submitting an amended return the best way for the taxpayer to complete an installment agreement is using IRS Direct Pay. It’s secure, free of charge, and available on IRS.gov.
Payments can be initiated in five easy steps and the taxpayer will receive a confirmation email when their payment has been submitted. A taxpayer must have a valid Social Security Number (SSN) or Individual Tax Identification Number (ITIN) to submit payments through the site.
Additional Information:
Form 9465 Installment Agreement Fees
General Information for Preparers Who File Returns Electronically