Are you saying this (using made up example numbers):
Traditional IRA after-tax contributions in prior years say $10k. No tax deductible contributions. Appreciation $5k, total $15k.
You convert say $6k to a Roth.
It sounds like you are reporting no taxable income because $10k has already been taxed and that is more than the $6k conversion.
That is not the way it works. Each dollar withdrawn from the traditional IRA (whether for conversion or spending) is part after tax and part taxable. In the above example the non taxable amount would be $6k times ($10k / $15k) = $4k. $2k would be taxable.
I do not know about NJ taxation so I can't help with that.
For the value of all IRAs TT is asking for the value of all of your own (not inherited) non-Roth IRAs. Why? Because it needs to determine the denominator of the calculation described above.
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