Just to clarify: The only TurboTax product that will prepare & file an S Corp 1120-S return is TurboTax Business. The various individual income tax versions of TurboTax -- such as Self Employed -- will only file your personal tax return.
Once you prepare an 1120-S with TurboTax Business software and each member is issued a Schedule K-1, then you enter your K-1 into the TurboTax individual software for inclusion with your personal 1040 return. You aren't able to prepare an 1120-S in TurboTax Self Employed; that's for sole proprietor's who report income & expenses on Schedule C of their 1040.
So I'm a little fuzzy on what you've prepared. It sounds like you've entered all your S Corp income & deductions into TurboTax Self Employed, which isn't what you need to do. Use TurboTax Business for the 1120-S, then enter the K-1 into the online software.
Lastly, you'll only need the Self Employed version if you have an additional business as a sole proprietor (with income on a 1099-MISC). If the S Corp is your only business, then TurboTax Premier will be able to handle the K-1 entry and any other personal deductions/credits that you have. You can certainly use Self Employed for that, but it's not required.
