Non deductible IRA contributions

I have 2 Traditional IRAs.  I have taken distributions from the 1st in tax year 2020, but not the 2nd.  In the 2nd IRA I have made a total of $12,000 of non-deductible contributions over the years and tracked them on the 8606.  In using Turbotax it asked if I made or tracked any non-deductible contributions.  I answered yes and put in the $12,000.  The program then subtracted the $12,000 from IRA #1 even though the non-deductibles applied to IRA #2.  Should I just not enter the $12,000 this year or does the IRS treat all IRAs as one and wants me to "use up" my tax free distribution as soon as possible.  Thank you.