I have had a few pups with CT with varying symptoms. What I have found out is the trial and error is the best way to deal with it. What works for one may not work for another.
There are many different meds that your vet can try ... if you feel this medicine is knocking him out too much, call the vet and let him/her know. You should not have to keep making appointments if it is just for a med change.
One interesting med that has worked for a couple of pups in the past is Lomotil (it is an anti diarrheal but works for CT in dogs sometimes).... it cannot be substituted with any other anti diarrheal. You might ask your vet about that.
Here is a link with some other options:
01 Tracheal Collapse - VeterinaryPartner.com - a VIN company!
I am assuming your vet probably discussed things with you such as keeping him relaxed, keeping his weight down, and not letting him overheat.
Welcome to YT! Please keep us posted on your baby.