My MacBook Pro, for example, has the usual built-in speakers for output, but I also have Audioengine's D3 DAC connected to a USB port. Once launched, you can choose any audio input or output available and make adjustments that go beyond the basic features in the Sound Preference Pane. You can find the Audio MIDI Setup app tucked away in Applications > Utilities. Even though Audio MIDI Setup may sound intimidating, it's loaded with controls that go far beyond what its name implies and can help you fine tune the audio quality your Mac pumps out.
Your Mac's Sound Preference Pane is the go-to place for choosing audio inputs and outputs, but it isn't the only place you can go in OS X to manage your Mac's sounds.