No, that question should not have come up after entering the Form 1099-R. Instead, you should have seen a question about what you did with the distribution. The answer to that question would have been that you converted it to a Roth IRA.
You will only have one Form 8606, unless you also have a spouse who has their own Form 8606. There will be two sections of the form filled out -- one for the non-deductible contribution and one for the Traditional to Roth conversion.
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