With port matching, you are simply removing any casting defects from your intake and exhaust flow paths, but it does not change the basic design assumptions of your engine.
With a little care and attention, this is a relatively 'safe' modification that can give you a slight, but measurable performance boost. For a more extreme engine mod, see port reshaping.
For more information on port matching, see Smitty's Cylinder Porting Guide.
For info on port timing, see calculating port timing.