If you’ve filed Form 941-X or another amended return, and you must make a tax payment for an old calendar quarter, you may use the IRS’ Electronic Federal Tax Payment System (EFTPS).
What to do: When you’re entering the type of tax to be paid, select one of these options:
- Balance Due on a Return or Notice
- Payment Due With an Amended or Adjusted Return
- Audit Adjustment.
Then, enter the tax period to which your payment should be applied.
AVOID LIFO: The IRS credits your tax deposits on a last-in, first-out, or LIFO, basis. If you instead select the Federal Tax Deposit option, the IRS will credit the payment to the current quarter, if its records don’t show that you have an outstanding liability for a prior quarter. Result: You will have an overdeposit for the current quarter and an underdeposit for the prior period, on which penalties and interest will begin to accrue.