The port closest to the firewall is for the front brakes.
Edit: I just looked at the Wilwood instructions at
http://www.wilwood.com/PDF/DataSheets/ds487'.pdf and it indicates the PRIMARY port is the port furthest from the firewall, and "Connect one of the primary outlet ports (A) to the brakes at the end of the vehicle with the greatest total effective piston bore area."
That's different than most dual / tandem master cylinders. When all else fails, read the manual. Wilwood documents can be downloaded from
http://www.wilwood.com/Pdf/PdfIndex.aspx
BTW, Wilwood primary and secondary ports appear to be different thread sizes (1/2" for primary and 9/16" for secondary) but I don't know if that applies to all MCs - best to check your specific model and if there's any doubt go straight to Wilwood for the answer.