IRA basis floats over all owned IRA accounts and is not assigned to any specific one, so as long as the amount being rolled into a qualified plan does not exceed the entire pre tax balance of all IRA accounts, no basis will be considered to have been rolled into the qualified plan. IRA aggregation rules apply consistent with Form 8606, so it does not matter which IRA receives a non deductible contribution OR which IRA account is rolled into the qualified plan. The tax code language in Sec 408(d)(3)(ii) is pretty murky, but the IRS cleared it up in Pub 590A here:

Tax treatment of a rollover from a traditional IRA to an eligible retirement plan other than an IRA.Ordinarily, when you have basis in your IRAs, any distribution is considered to include both nontaxable and taxable amounts. Without a special rule, the nontaxable portion of such a distribution could not be rolled over. However, a special rule treats a distribution you roll over into an eligible retirement plan as including only otherwise taxable amounts if the amount you either leave in your IRAs or do not roll over is at least equal to your basis. The effect of this special rule is to make the amount in your traditional IRAs that you can roll over to an eligible retirement plan as large as possible.

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