I personally have used both protocols and have ended up using the zapper and anti parasite herbs of Dr. Clark's protocol primarily, and the electromagnetic pulser from Dr. Beck's protocol. The Clark protocol has definitely rid me of the parasites causing diabetes, and I am not bothered by diabetes any more, and the Beck pulser is like magic for killing bacteria and virus. I can't recommend it enough. It should totally be available at all hospitals!
I found that neither protocol work with fungus though. But luckily olive leaf extract does, for the lungs and throat and a silver based product called terrasil max works for the external fungus, although the company has had keep the silver low key, in among the other ingredients since the FDA is being a bunch of asshats about silver.
The Beck protocol seems a bit unwieldy over all though. Too many steps. And it doesn't really address the parasite issue, which I have found to be one of the most undealt with problems in modern society. Plus Dr. Clark's work is easier and quicker, and has worked well for me. Those who say it doesn't work usually haven't done the whole process, I've found. You have to do the herbs for the initial recommended 2 week parasite cleanse AND the zapper. And then make sure to follow up with the herbs once a week and zapping once a week.