Box 5 lists Designated Roth Contributions. That amount is deducted from Box 1 (Total Wages) and remainder is listed in Box 2 (Taxable Wages). Do I report the Roth somewhere (there is no appropriate Box 5) and which wages value do I report?

[MichaelL1]

You enter the 1099R exactly as it was received. 

Box 5 can be a number of different things:  Employee contributions/Designated ROTH contributions or Insurance Premiums. 

Due to box 2a already being reduced, you do not need to the enter the amount from box 5 anywhere else in the program.