"Can I handle the basis calculations as if the two IRAs were still one, summing the two IRA year-end values for the basis calculation, as for the RMD calculation?"
Not only can you do so, the tax code requires you to do so, treating your traditional IRAs as a single account for this purpose. All of your traditional IRA distributions (except for Qualified Charitable Distributions, HSA Funding Distributions, amounts rolled over, recharacterizations of contributions and returns of contributions; of these, someone subject to RMDs would probably only potentially do a QCD), basis and total year-end value of your traditional IRAs are included on a single Form 8606 Part I for calculating the taxable and nontaxable amounts of distributions. The answers provided by the others indicate how TurboTax takes the input that TurboTax places on Form 8606.
