TurboTax has no shortcut to do this and there is no absolutely right way to do this. One method is to prepare separate (not married filing separately) returns for each and use the total taxes on each return to manually allocate the joint tax. Actual withholding is then used. Certain items can create issues with this method. With online, there is only 1 return per account, and you can't see the numbers in detail until you pay all fees.
