Why is my federal taxable income different than my state taxable income?

Very common.  Federal and State have different deductions, so your taxable income wont always be the same.

How do I deal with the State form that automatically enters the state taxable income from my federal form that is much greater than the state taxable income on my w-2

There are different deduction amounts must be considered. Standard deductions for federal returns are much different than they are for state returns.  have you have a chance to look at your federal and state forms, look to see how each state's taxable income was calculated. .