It's a safe bet to say a sound card is always going to be better, but it does depend on the listener and what you are using in the way of headphones or speakers as people's experiences vary.
If you can fit the sound card with no trouble, then I'd go with that. If you're going to run into space or heating issues with GPUs, then as you've already got the sound card, try the onbard audio first and decide for yourself whether you think it sounds good enough.