+Harold.
Exposing the live rock portion to the ammonia is counterproductive but not destructive to live rock, it will oxidize large amounts. But we adapt animals on that pricey surface to no free ammonia (corals, crabs, feather dusters, stars, sponges, pods all the live rock items we pay for and good coralline. Mostly live rock is base rock sat in water for months and not diverse, not inclusive of lots of life just two spots of coralline if lucky)
Free ammonia is for dry substrate cycling. We pay extra for live rock so we don't expose it to free ammonia
Accurate cycling would say leave the dry rock in there to catch up add no ammonia. Plan the max bioload for the tank around the known live portion, the dry substrate just sits there.
Actually your type of tank is ideal for a fourth kind of cycling description update to this thread, will call it the blended cycle. It will fit exactly in line with the opposing treatments detailed in the post here
http://reef2reef.com/threads/new-ta...d-cocktail-shrimp-live-rock-no-shrimp.214618/
Adding bottle booster bacteria is completely ok and probably will speed up the dry rock cycle portion. The reason no ammonia needs to be added is because the live rock portion is a respiring collective
Respiration=ammonia down the chain in the exact micro amounts it takes for live rock to be self sustenant for a very long time
The dry rock portion simply takes on coralline and benthic castings from the live portion over time whether you speed it up or not. Blended cycling is a worthy division within common reef tank cycling approaches nice example here.