You're definitely better off disabling the onboard soundcard as it may conflict with the Audigy. As for the front audio ports, they may have cables connected to them that are run to the MB. You could just disconnect them and run them to the Audigy if it has the available pins. Also, you're right, once you disable the onboard from the bios, the front ports will not work unless you reconnect them to your Audigy somehow.

Andy