You must enter your year-end balance in traditional IRAs and your wife's year-end balance in traditional IRAs separately. IRAs are individual accounts, not joint accounts, and all calculations regarding the taxable amount of any of an individual's IRAs must be done entirely separately for each individual.
There is no such thing as a "non-deductible IRA." All of an individual;s IRAs are treated as a single combined IRA for the purpose of determining the taxable amount of any distribution from any of the individual's IRAs. It doesn't matter which IRA of the individual the distribution of a given amount comes from, the nontaxable and taxable amounts are the same.
