If you're just using it in a second cup, to create an airspace under the first cup, then you're ace. This is a perfectly legit setup. I originally understood that you were putting the hydroton in the bottom of a single cup with the grow media layered above it.
You don't need to worry too much about salt build-ups, if you're dosing at moderate quantities. Many of the weed growing dinguses think that the more nutrient they throw at their plants, the better their "yield". They're always on the high side (no pun intended) of the nutrient dose, so they often have problems with salt build-up. But the rest of us will most likely never see a salt build-up issue, if we're dosing normally. And the run-off for watering is good if it fits a system. But once you start using coco like soil - especially outdoors - you treat it the same. Just water as necessary. It's typically better not to saturate, but coco built mixes are VERY tolerant of saturation watering. Much more so, in my experience, than peat. (if there is a drainage amendment - and 25-30% perlite is a winning ratio)
Don't be afraid to bottom water. I actually like to use both methods. I'll sometimes bottom feed young plants, but spritz the top of the media. That really works well for me. But if what you have works, roll with it, just the same...