I noticed the tadpoles in our DWC and never considered they would eventually feast on the roots of our plants. When it became obvious the plants were not doing well, I discovered the roots were gone beyond the bottom of the raft. I did a little reading and found that the tadpoles are omnivores. To eliminate the tadpoles I put some catfish in the DWC and the tadpole problem was solved in a matter of days. Now the problem of how do I feed the catfish in the DWC. My bright idea was to catch the catfish, put them back in the FT and get some goldfish to reside in the DWC for tadpole and mosquito larvae control. The goldfish do a good job eliminating those pest, but now they are munching on the plant roots. They too are omnivores. A few days have passed since I put a catfish in the tank, this time to eat the goldfish. So far the goldfish have survived.
I would leave only one or two catfish in the raft tank. You may have to catch the goldfish yourself, if the catfish are well fed, they won't work hard enough to eat the goldfish.
Okay, I caught 7 of the 9 goldfish and put them into the FT. There was a distinct look of concern in their eyes when I went back to check on them. The catfish, on the other hand, were welcoming the new guys. "Come on in. The water is fine." The one catfish in the DWC will remain there, along with the other two stubborn goldfish, to patrol for pests. Thanks again.
Oh, wow, it sounds like you're making an ecosystem there. Keep in mind that fish, or tadpoles, eating some plant roots won't really effect the plants, if put in check. I would put carnivorous fish into there after you get rid of the goldfish and put the catfish back in the main tank. (Warning: this is not based on practical experience, but theory based on High School Biology.)
channel catfish are not very likely to eat plant roots if there is any other food for them. Even if there isn't much food for them, they are not that keen on plants even if they are counted as omnivores.
Oh, Catfish seem like a perfect species for this job, then.