Mike,
Hi, are you filtering out the old rotifer water before you add the rots to the baby clownfish tank? You want to get rid of the water the rots have been growing in.
I do the filter thing, and then I let the concentrated rots sit in a bowl of phyto for a 20-30 mins. They eat fast and fill up with phyto, then I filter them out of that soup and feed the rots to the larvae. I just rinse them off the screen with a little larvae tank water, and then pour them in gently. Then add live greenwater to tint the larvae tank green or make it a little cloudy.
I have found, like you, that the larvae tank does not need too many more additions as the rots like the larvae tank conditions and multiply faster than the larvae can eat them. But watch out if you get a really big number of clownfish larvae that hatch. They may be able to consume the rot population faster.