Aeration is one of the key steps to follow. But it isn't to add O2, it is to help with gas exchange and buildup of CO2.
Any of you who have used ChemiClean and have a pH monitor in your system probably noticed a pretty sharp drop in pH when you used ChemiClean. That is a sharp buildup of CO2. Now think about how a calcium reactor works, inject CO2 into the reactor, carbonic acid forms, and dissolves the aragonite releasing the calcium.
IMHO the instances where people have trouble with ChemiClean is from that sharp decrease in pH.
This is the ritual me and my family/friends follow if we use ChemiClean.
1) Manually remove as much cyano as possible
When the cyano dies off it releases a small amount of toxins into the water, if you have a lot in the system when you start it could cause problems. Since you can't use carbon while the treatment is ongoing there is nothing to remove them. This can be compounded by the corals (especially softies and Zoas) releasing toxins from stress.
2) Get the dose right
3) For an in sump skimmer, remove the cup and set it wide open (if not use a large air stone and air pump)
It's critical to keep a lot of gas exchange going during the whole process
4) Add the dose slowly
It seems to be less of a shock to the system if you add the dose over the course of a few hours, the liquid Chemiclean is great for this, but you can do it with the dissolved powder too.
5) Blackout the tank and sump during the treatment
This seems to increase the effectiveness of the treatment and lowers the stress for the critters.
6) At the end of treatment do a 25% WC and add GAC back to the system
We've done the WC by putting the cup back on the skimmer and running a line from it to a bucket to remove the water and let it skim super wet. This seems to accelerate the removal of the remaining Chemiclean.