So I paid my contractor directly for first job and then every job afterwards bill was entered and payed through direct deposit in Quickbooks. Is there a way put that first job in Quickbooks and mark it as paid so that I have record of it when I do 1099?
You can set up your contractors as vendors, then create a bill transaction and pay it to mark it as paid. This way, you can track your payments for 1099s in QuickBooks. Let me guide you through the process.