If I have to glue a polyp directly, I put it in water asap so that the heat from the glue curing is dissipated so as to not burn the polyp. I use a small bowl of tank water to do this, once the glue sets I move it back to the tank. Like Manoj said, try to put it in a spot that it isn't going to get blasted off whatever you glued it to.

I like to presoak the plugs or rocks in tank water (in the bowl of water mentioned above). In the case of ceramic plugs, it gets the air out of the plug so it doesn't bubble up through the super glue. It also helps the glue bond to the plug (or rock) better.