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-When I fill out a form for both of us, then trying to report IRA contributions, then it says I contribute too much (12K, but then says I contributed 6K too much).

you must indicate that $6k is for your IRA and $6K is for your spouse's. you can not contribute $12K to your IRA. so she needs her own account 

 

-When I fill out a form separately, then I don't know what to do about our joint deductions - Do we both fill in what we pay on property taxes? Or divide it by two? expenses must be split otherwise you are double dipping which the IRS strongly frowns upon.