In State section, there is one page for you to enter estimated tax payment amounts and dates. Enter $800 and the date that you paid here. Afterwards Turbotax Business will not show that you owe $800 and penalty any more.

If you have already paid the annual CA franchise fee and it is not showing on your state return. You can manually enter the amount on the State Taxes section. If you are using TurboTax Business, please click on the the California S Corporation tab under the State Taxes section. You will need to go through the interview pages until you come to Review Schedule M-2 page. (see attached screen print file)

Once you are at the page, use the scroll up arrow to Line 12 box. There, you will enter the amount paid for the franchise tax and include other deductions if the program is not picking it up. Then, click Continue to save your work.

I believe I have followed the directions correctly but I continue to receive indications that I owe $800 plus a $29 penalty.  I have spent a couple hours in this area and cannot figure out what I'm doing wrong.  Where is the calculation performed that determines that one owes these amounts?