I think that depends on your sound card. I'm not 100% sure, but I believe on my setup which uses a Creative Audigy sound card, the only way to get multichannel DVD sound to my 4.1 speakers was using the proper DVD player software.
On the other hand, if your speakers use a digital connection rather than analog, then any DVD software will pass the multichannel signal out of the sound card's digital output where it will be decoded by the decoder in the digital speakers.
So I guess a lot of it boils down to which sound card and speakers you are using.