actually, it's not supposed to be better. just faster. the available software is very basic. you aren't going to find anything that lets you do the load balancing yourself. in fact this software niche is so immature right now that we are basically struggling for high quality output.
cyberlink's mediashow espresso is the only complete software suite that works with ATI and nvidia hardware, and in my opinion it's only good for transcoding to mobile devices, because the low resolution allows you to hide much of the crappy quality. I haven't used it myself, I've only read reviews and seen screenshots of various outputs. If you want my advice, continue to do your high-quality encodes on x86 with x264 using handbrake, automkv, etc. If you have mobile devices that you can transcode to, then go ahead and experiment with GPU encoding. It's come a long way but we still aren't there yet (remember anand's article? he couldn't even get the audio to sync).
This is probably the best article to start with
http://www.legitreviews.com/article/978/1/