To avoid one or the other tax returns having an underpayment penalty, it might be necessary to split the estimated tax payments between the two separate tax returns. When filing separately, each separate return is allocated a portion of the previous year's tax liability in proportions that would be the same as what the proportions would have been if the previous year's taxes has been filed separately. For example if when filed separately one spouse would have had twice tax liability of the other, the safe-harbor for the spouse with twice the tax liability would be determined by 2/3 of the previous year's tax liability and the safe-harbor for the other spouse would be determined by 1/3 of the previous year's tax liability (the same 2:1 ratio). More details are in IRS Pub 505.
