You don't. Tell the client to pay what they can at https://www.irs.gov/payments/direct-pay-with-bank-account Tell they to pay the balance (or what they can) as soon as possible. They will be bill for interest and late payment penalty. Use the program only for full pay. You can enter an amount for the amount on the to be paid via the program on due date in the Form 1040 payment (defaults to amount due)[Override] but beyond that it is on the taxpayer to take care of it. My opinion - make they do all the payments and don't use the program to do any. 

Alternatively file for an extension and have the payment taken out when filed.