For tax purposes, you only have one Traditional IRA which is the aggregate total of all existing IRA accounts. The non-deducible basis applies to the overall aggregate IRA total. It also does not matter which IRA account or accounts the RMD is taken from since the total years RMD amount is based on that aggregate total value as of the end of the previous year.
When calculating the non-taxable portion of your RMD on Form 8606, all of your IRA Accounts (Excluding Roth) are taken into account regardless of whether they are made up of Deductible or Non-Deductible Contributions. For more information, you can click this link to see IRS Pub 590, Distributions from IRA's starting on Page 13.
Use Form 8606 to track the basis of your non-deductible contributions when you:
- Take distributions from a Roth IRA
- Take distributions from a traditional, SEP or SIMPLE IRA at any time after you have made nondeductible IRA contributions
- Convert a traditional, SEP or SIMPLE IRA into a Roth IRA