If I recall correctly, he broke is ankle, so he most likely have both knees down since he probably could put too much weight on his ankle(whichever one he broke). I can't imagine he would be set up in any other way.
If I were doing his type of long toss(how I envision it would be set up), would be on both knees with my chest facing my target, maybe at a slight angle in.
Look at your mechanics as you do any type of throwing program. Improving your mechanics will help(I would argue more) than long tossing by itself. There is something to be said for going out and throwing with a high level of intent, but if you're able to make yourself more efficient while using high inent, you're going to be all the better from it.
Interesting that you mention his long tossing from the article about him. I have been considering a throwing program that uses long tossing using his method, so it's easier to do indoors with limited space.