Yes, when you start taking distributions from your IRA, you will then need to adjust your basis in your IRA and include any such adjustment on Form 8606. The adjustment you will make will take into account the after-tax money you contributed to your 401(k). Keep your records for when you will need to make the necessary adjustment.
Thus, for now, do not enter the after-tax contributions you made to your 401(k) on Form 8606. Form 8606 deals with non-deductible contributions to traditional IRAs, conversions of IRAs to Roth IRAs, and distributions from Roth IRAs. It does not concern rollovers of a 401(k) to a new IRA.
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