Get your taxes done using TurboTax

It depends.

Did you make the input in the federal interview section of the program or only in the state interview sections?

Be sure to enter the overall amounts in the 1099-INT or 1099-DIV section of the federal interview depending upon what form your tax exempt income is reported on.  

You will have a screen that allows you to break it out by state.  As long as you break out the amounts for the state returns you are filing in, you will be okay.  Be sure to enter the rest as being from Multiple states.  This will be the last option when you select your state return.

When you get to your state return(s), you may have to enter your state specific information here as well.