TurboTax handles this if entered correctly. You must enter the simulated Form 1099-R, indicate that you moved the money to another retirement account, indicate that you did a combination of cashing out, rolling over, and converting, then indicate the amount converted (presumably the entire amount). TurboTax will exclude the converted amount from line 1 of TurboTax's Roth IRA Contribution Limit Worksheet.
Note that any amount of an In-plan Roth Rollover within an employer plan like a 401(k) is not permitted to be excluded. (A designated Roth account in a qualified retirement plan like a 401(k) is not a Roth IRA.)
