How I am supposed to send back the refund that I have received as a result of the wrong tax return form?

I'll receive the refund that I'm supposed not to receive, and I would like to send it back with amended tax return. 

Can I send back the paper check that the IRS has sent to my address with the new return and a check for the money I owe?

Or should I make separate paper checks, the one is for the amount I have received from the IRS, and the other one is for the amount I owe? and send them with the new return?    

Thank you