Again you NEVER have to enter the 1099 income in the 1099 section of the Sch C income entry screen ... the only reason there are 3 places to enter Sch C income in the program is because if there wasn't the uneducated users would be confused. So again you don't have to enter in the 1099 income at all since none of it goes to the IRS at all ever (the IRS gets a copy of the 1099 from the issuer just like you do ) ... all the IRS ever sees is the total on the Sch C. If you want to use that section go ahead ... it is your time to waste.
