Notice 2014-54 only applies to distributions from qualified retirement plans like your 401(k) , not to distributions from IRAs. Any distribution from your IRA will be a pro-rata distribution of taxable and nontaxable amounts in the proportion that the after-tax money (now treated as contribution basis in your IRAs) makes to the overall balance in your IRAs and is calculated on Form 8606. You're after-tax basis from the 401(k) is entered into TurboTax by indicating, Yes, you made nondeductible contributions to your traditional IRAs, then clicking the EasyGuide button and indicating that you rolled over after-tax money from an employer plan. TurboTax will then ask you to provide an explanation statement for this adjustment to your traditional IRA contribution basis that goes on Form 8606 line 2.
The only way to isolate basis in your IRAs would be to roll the pre-tax portion to a qualified retirement plan that will accept such a rollover. Rollovers from an IRA to a qualified retirement plan are deemed to first come from the taxable money.
