you can let all digital data go through either coax or fiber optic (the latter being better), and specify it on your receiver as DVD and regardless of what kind of disc you put in your dvd player, it will play. HOWEVER, this means your receiver is converting the 1's and 0's into analog.

If you run the L/R cables, then your DVD player is converting it.

Try both and see what you like. Usually a DVD players' CD audio section isn't very good, which is why most people let their receiver do the conversion.

try both (if you have the wires for it) and see which one you prefer.