Do I enter the Paying Agent name and address or the Retirement Plan company name from my 1099-R as payer?

You should enter the paying agent that is listed on the Form 1099R when you complete the form in TurboTax.  The EIN listed on the form is an identifier of the payer so it's important that the EIN and the payer's name match.

I was currently rejected for my 1099-r not having the correct EIN. 

My issue is when entering the information it doesn't ask for EIN  only the payers TIN.

The 1099-R I received doesn't even have a EIN on the form.