All of Jim Humble's original protocols (numbered) use activated MMS (alias MMS1 in common parlance); Andreas's protocols (lettered) generally use CDS although Protocol B is clearly described in terms of [activated] MMS although he provides a conversion to CDS at the end. I understand Andreas's intention is to provide parallel treatment protocols using CDS, which Andreas views as better, rather than the activated MMS.
Don't get too hung up about the different protocols; they are not magic. The important thing is to get the ClO₂ into your body on a regular basis at sufficient dose to have good effect and below the threshold where the Herxheimer reaction causes discomfort. This is citizen science; citizen medicine. Read up on the options, experiment, feed back, develop what works in your situation.
With a disease like arthritis, depending which joints it is affecting, it could take significant time to effect a change. With finger joints (as troubled Andreas), changes might be seen quite quickly whereas a large, load-bearing joint like a hip will likely take months before an effect can be detected.