MMS will get into all the "cracks and crevices" in your body over time...as you said, it works upon what it comes in contact with. It will continue to be carried deeper and deeper into the tissues and organs until it encounters more organisms or substances that fit its target profile.
I can tell you from my own personal experience, and the experiences of many others, that sodium chlorite WILL absolutely clean out the entire body over a period of time. Of course, it needs to be complemented by hydration to flush out the toxins, and by lifestyle changes too.