The nontaxable amount shown on line 12 applies to the distributions in aggregate, not to any one particular distribution. While the amount technically applies proportionately to each distribution, because these distributions get combined everywhere on your daughter's tax return, it doesn't really matter which distribution's gross amount you reduce for the purpose of reporting the taxable amount. While (because the basis in nondeductible traditional IRA contributions your daughter as beneficiary, not to any particular one of the inherited IRAs) it's technically incorrect to answer for one Form 1099-R that you wife had basis and for the other that your wife did not have basis, doing what you propose will produce the same taxable result as entering the taxable amounts correctly (proportionately).
