On my 1099R is my employee the Payer or the paying agent?

Who issued the 1099-R? A pension plan? An IRA custodian? An insurance company?

The Payer is whoever issued the distribution that the 1099-R is reporting.

I do not know what you mean about "your employee" and "my 1099-R".

Are you trying to prepare a 1099R to give to your employee?  Why?  The 1099R come from the pension plan or 401K etc.  They are the payer, not the employee.  

Or did you mean is your EMPLOYER the payer?