Simple is always beter ... the S-Corp election was approved for the start of the year so all your business income and expenses should be on the 1120-S. You need to let everyone know that you are now a corp for the entire year and give them a new W-9 form indicating this so IF they do issue a 1099 it goes to the corp and not you personally. (FYI a 1099 is not required to be issued to an S-Corp however some will issue one anyway)
IF you do get a 1099 issued to the SS# and the issuer will not correct it then simply put the income on the Sch C like you did in the past then do an expense of the same amount to negate the income that you will report on the 120-S.
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As for payroll ... the IRS acceptance notice tells you exactly which forms you need to file an when which includes the payroll forms 940 & 941 ... payroll should start this quarter (third) filed in October.
This answer has been verified for accuracy by an Intuit expert employee
