I just skimmed the link--looks like a good program. I want to add some running to my routine once it warms up a bit, so I may incorporate some ideas from that. Right now I follow the same principle they mention of 20-30 minutes 3 times a week, except I was doing it through rowing this summer, and now that it's cold out I do it indoors through the cardiokickboxing routine I mentioned a buncha posts back, which is basically 4 sets of a sequence of punches, angled punches, pivoting blocks, and kicks followed up with sets of sit-ups, push-ups, and bicep/tricep curls. In addition to that I do a Tai Chi type thing every morning when I wake up for about 40-60 minutes, followed by some Yoga-type stretching. Seems to be working pretty good for me as long as I stick with it, but if I miss a day and get out of my routine the hard part is getting back into it.
Regarding Atkins, one of my online training partners is on that, too. He's lost about 50 pounds so far. The only problem he had was that at a certain point he was getting brittle skin on his fingertips, but that went away once he started taking some nutrient supplements.