No. You can have both on-board (motherboard sound) and a separate sound card installed on the same PC but you will need to tell your software which device you want to use. You can set system wide defaults by going to the Sound Settings in the Control Panel and selecting the device you want to use for default Recording and Playback. To override these settings most software will require you to enter this information in to the program preferences.

The examples below use a Creative SB X-Fi sound card and High Definition Audio on-board sound:

Winamp 5.5 Input / Output Settings



Mixcraft 4 Input / Output Settings