I've visited China through Beijing and Hong Kong numerous times over the last couple years, and without a doubt the best way to do it is through a Visa intermediary such as travisa.com or A Briggs (http://www.abriggs.com). I've used others in the past, but we had an emergency trip about a year ago where one of our fellow travelers needed to go at the last minute (ie, we were leaving on Weds, and they decided to go on the Sunday before), and A Briggs helped us get them a passport and the Chinese Visa, and had it waiting at the airport for our departure. They also have agents you deal with directly.

I'll definitely use them again. The point though, is that for a nominal fee, it's just easier to have someone who does visas every day handle the China situation for you, at least in my experience.