Received late 1099Misc, how do I make correction?

My wife works for a company that is a dealership. I did my taxes over the weekend and filed. After filing (2 days ago) she received a 1099 Misc from the manufacturer because some of her bonuses were received directly from the manufacturer (unbeknownst to me). Brief version is I submitted my taxes without claiming the $675 1099 Misc. 

The IRS website says "If you realize you made a mistake but the due date for filing hasn’t passed, do not file an amended return. Instead, file another original return with the correct information." 

Is there a way to E-File this? To be honest, an audit would be a nightmare. I have $60,000 in deductions the last three years, I have all the info but am dreading the nightmare.