Like funkytuna said, the audio is passing over the IDE cable, so don't worry about the physical configuration of your drive.
What you need to do is look at the audio settings in the software you are using for DVD playback. It's probably set to decode 5.1 dolby digital, but you only have 2 speakers. You need to change it to downmix to 2-channel stereo instead.
It also wouldn't hurt to check the settings in Windows too. Under the Control Panel, double-click "Sounds and Audio Devices". Depending on your sound card hardware, the settings here will vary, but see if you have an advanced settings for the speakers. Make sure Windows is set to use "desktop stereo speakers" if you see that setting.
~cdogg
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