They dont wire up to the motherboard at all....the only connection is an ide type connection between the soundcard and there is a 4 pin power connection to the drive bay as well as the fps version of the card. You may also connect an audio wire to your cd roms but it is not required. Its pretty simply. The front panel is great for headphone use.
I have a first generation Audigy with the drive bay, and if nothing has changed it is really, really easy to wire up. It takes power right from the power supply (3.5" floppy power, comes with an adapted if you don't have another floppy power connector) and has a special IDE like ribbon cable that comes with the card that goes from the card to the drive bay that comes with it.
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