All of your traditional IRAs are treated together as one large IRA for the purpose of determining the taxable amount of any distribution, including a Roth conversion. This means that the balance in the rollover IRA must be included on line 6 of Form 8606 in determining the taxable amount of any Roth conversion. Presumably the rollover IRA has much more than would be in the new traditional IRA, so the Roth conversion would be mostly taxable, which most of your basis in nondeductible traditional IRA contributions remaining with your traditional IRAs to be applied proportionately to future distributions. The fact that the nondeductible contribution is made to a different traditional IRA than the rollover IRA is irrelevant.
