1. The payment with the 9465 will be credited and penalty & interest will accrue on the balanc

2. Interest and late payment penalty will accrue of any balance by, determined by the payment dates. The client can make payments at https://www.irs.gov/payments/direct-pay

Did you do a 2210 with the return? There could also be underpayment penalty due. 

Generally if the client can pay in a few months I DO NOT send a 9465. I just have client send money just like you are doing. The 9465 makes it too formal for such a short period. The IRS may not even finish processing a 1040 in the few months the client might take to pay off the tax.

I suggest the client set up an IRS account so they can check on the posting of the return and payments. https://www.irs.gov/payments/your-online-account set up the account there. 

If you did the 9465 with automatic debit, then have the client be sure there are funds in the account for the dates you set up.