I have been noticing more and more large brand retailers launch customized QR Code campaigns with an embedded graphic. It's definitely slick from a brand marketing and mobile marketing standpoint. So how do they do it? I did some research and here is what I found (Link, excellent article with lots of samples).
In short, the way it works is that QR codes have up to 30% of error correction built in. Essentially, a graphic artist would have to overlay the branding element and try to match as many pixel as possible. It sounds like intense labor but given the high % in error correction, it seems like it isn't all that difficult. I used GIMP to play around with a QR Code and it worked just fine!