To do a real "back door" Roth conversion, you have to convert all your traditional IRA balances. For example, suppose you make a $6000 non-deductible contribution this year. If you convert the entire amount ($13,000), then 53% of the balance is taxable. That's the $7000 that was never previously taxed, because it was a deductible contribution or tax-free growth. Then in the future, you can make a $6000 non-deductible contribution and immediately convert it tax-free.
However, if you make a $6000 non-deductible contribution this year, and only convert $6000, you will still pay tax on 53% of the conversion, because when you do a conversion, the taxable part is determined by your combined balance of all traditional IRAs. And that would leave you with a $7000 balance that was partly taxes and partly tax-free, and you have to keep track of your basis on form 8606.
So really, convert all you traditional IRA balances or it isn't really a back door Roth.
