That's what I do.
I take a chunk of rock that I'll be putting the frag on and superglue the zoos directly to the rock. I wouldn't worry, zoos are hardy and it won't kill them to touch the superglue. I would kind of shake the zoos a little while they're under water to make sure they close up completely before taking them out of the water but maybe it's not necessary. Then you can superglue directly to the smaller rock. Then I mix a small amount of putty into a coin size. Then I put a nice layer of superglue gel on one side of the putty and put the superglued side on the underside of the rock. Then press it in place firmly. Then I put another layer of superglue on the other side of the putty (which is now the underside of the small rock) and then stick in in the tank where I want to put it. Be kind of quick because the longer the gel superglue is exposed to water the faster it will set.
Doing it this way keeps me from using too much putty and helps it hold better than superglue alone.