The space allotted for diffusion within a vile is minimal, so yes, it will require gentle agitation to mix the chemicals. You shouldn't have to shake, just re-cap the vile, and turn over 3-5 times until the chemicals have diffused evenly within the water sample. I usually do 2-3 drops at a time, then re-cap and turn over a few times, then as it changes, start doing 1-2 at a time.
Was there another question you had? I couldn't figure out if you were just explaining what you're doing, or had a question in there somewhere, let me know.