Yes, in general, spouses can agree on how to allocate payments made with a joint return when filing amended separate returns. Treasury Regulation § 1.6015(b)-1(b) supports this approach for estimated payments, and the IRS typically allows spouses to split prior joint payments as they agree. You don’t have to claim the full amount on one return—splitting it to reflect your $0 and your spouse’s $3 liability is reasonable and in line with IRS practice, though you may want to document your allocation in case of any IRS questions.
