As long as you report the cost basis correctly, it won't make any difference if you use the Stock (non-employee) route. The IRS really doesn't care how you got the stock, just that you report the proceeds, cost basis and holding periods correctly.
The reason the TurboTax program prompts for Employee stock (ESPP, NQSQ, ISO, RSU, etc.) is to make sure you look in all the right places to accurately calculate your cost basis and holding period.
