If he get a W-2 form the church (most pastors) and also has side income, report the side income on a self-employment business -- he is in the same situation as an employee who "moonlights" as an independent contractor in the same field. Set up the self employed business using occupation code 813000. You will be asked first about any 1099-MISC, but later you can enter "other income not on a 1099-MISC".
