(Begin Preaching) First of all if they are doing accounting between them on their refunds/taxes that does not sound like they are a "WE" yet. 

Statistics show that if the keep their money as "Mine" and "Yours" that their marriage ends up with great challenges. (End preaching)

That being said. I do a spreadsheet (often by hand on a 4 column pad, for those that still know what that is) Column 1 Total, 2 his. 3 hers, for all the lines of income and expense and withholding. If there is SE tax that is also allocated to each by their portion.

Tax is allocated by the percentage of net of Income and expense for each and compared with the withholding.

I just find it easier and quicker to do it by hand than try to find another way.