a theoretical way would be to buy the desktop software. and then prepare two returns as if married filing separately. if the joint return used itemized deductions you both are going to have to agree on a method to split them. from this there are several options.
1) line 20 or 23 would show either or both owed or were due as a ref. it is possible one of you would owe and one would be due a refund. This works best if the total from line 16 on each return is the same as line 16 on the joint return.
2) if this isn't the case you could use the taxable income (line 11b) from one MFS return divided by the total of that line from both returns. use that ratio to split the tax on line 12a on the joint return. after this use take the pro-rated tax and add additional taxes and subtract additional credits that each is responsible for. from this subtract that person's withholding and their share of estimated taxes. if estimated taxes were paid then again you both are going to have to agree on who gets credit for them.
again there is nothing in the laws about these methods. There are others. these are just a few of the ways that pro's suggest when they have taxpayers in the same position. of course, some pro's have the software that can do these computations automatically.
