No, you leave the original rfa file(s) untouched and you place your patched rfa on the server. The client (ie your pc) should remain unchanged - thats the point of a server side mod... the client doesnt need to download a new map before hand.
The patched rfa is the one containing your changes, eg a modified objectspawns.con etc, and should in theory be quite small in size. There is a naming convention to follow when it comes to file names: map_name_00x.rfa, where x is a sequence number that increments by one with every patch. So for example, the default map might be coolmap.rfa, and your patch would be coolmap_001.rfa.
There is a good explanation of this in the forum already. A is worth a thousand words
