Well tehre will be actually, and I've used onboard against real sound in a PCI slot.
The motherboard audio tends to use more resources, i.e your CPU, which can really affect it. For instance I have a Realtek on mine, which is a 5 channel audio inbuilt. Now, the computer when it was doing something that needed the CPU, cut off the sound and made it jump because it couldn't get enough resources to run the sound, and this will happen in games and other applications too.
I would advise to get a sound card dedicated to it, that won't use an resources. So I would definetly go for it