I typically do the same thing as many of my songs switch between clean, distortion, lead, etc all in the one song with many different effects and therefore I would plan to have the bottom row of buttons as presets and the top row of buttons as stomps. I can't imagine doing it any other way in an effective manner. Having quick changing presets is particularly important when going between clean and distortion sounds and vice versa in one song.
Since I would be switching channels on my amp with the helix via midi would this be instantaneous even if the fx haven't loaded yet?