If I'm not mistaken, it's not a good idea to swallow the MMS2 capsules with MMS1. If I am, then someone can correct me on that.
Anyway, I've just recently come up with a protocol of my own. Before, I had the intent of doing the 3-drop doses for 8 hours, but found that I was pretty bad about it. I'd get lazy and end up only doing a few doses per day -- not to mention the fact that I can't make doses while I'm not home. So now I'm doing a 6:6-4-6:6 kind of deal -- or a 12:4:12. It's a 6-drop dose, then another one in an hour, the MMS2 capsules every other hour, then another 6 & 6 at night. It's a nice structure, and it separates the MMS1 and MMS2 very well.
That's just my suggestion, unless of course your condition is life-threatening in which case you should do Protocol 2000.