You should at least disable the onboard in windows.
My sound card worked fine with it left enabled in the BIOS until I installed the game Stubbs the zombie and it had no sound for some reason. Disabled the onboard in the BIOS and it worked fine, which was strange since sound worked fine in everything else.
If you dont even disable the onboard in windows, it may still work ok, but you will probably at least have to select the new card in control panel/sounds and audio devices/audio tab and setting it as the default device for each option.
Its probably best to disable it in the BIOS just to be sure, windows will no longer see the hardware and will use the sound card by default. If the system still tries to load some kind of audio software for the onboard audio (icon in the system tray or error on startup) then it would be best to uninstall its drivers/software in windows also.
Once you install the sound card then you wont be using the onboard audio any more, so the audio ports on the front of your case wont work unless you disconnect the wires that run from the mobo to those ports and plug them onto the correct places on the sound card (assuming that card has those connectors, it probably does).
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