You need to tell the program what your basis in the Roth IRA is. Converting after-tax 401(k) contributions to a Roth IRA is not common, so the program provide that scenario. Either method you describe will allow you to enter your Roth basis, which is all your trying to accomplish. I would choose the first and indicate that you made prior Roth contributions. You're not making a statement that will be reported on your tax return, just trying to get some information into the program so it calculates things correctly. There are no other "side-effects".
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