I wouldn't worry too much about whether you are getting the baytril in the "windpipe".
If you are able to open the chameleons mouth (mild pressure to the commisures of the mouth(most outer lips)) you will notice a little tubular projection from the bottom of the mouth. It's not as pronounced as a snake, but is easily observed. Try to put the syringe of medicine behind this in your golden...okay, you freak out and squeeze the syringe early and it gets into the windpipe no biggie...This is a pretty badass antibiotic (fluoroquinalone). If diluted is usually with sterile saline. So aspirations pnuemonia will be killed before it even begins. My guess is that the dilution that your vet gave you is like .1 or .2 mls. If so, draw up water and put this amount in your hand...it is not enough to cause any choking.
I'd be more worried about stressing out the cham by giving meds, so don't screw around when you are administering it. Get the cham, give the meds, put him/her back in the cage. By hestitating and not doing it decidedly the first time, you will stress out the cham more.
As far as injections of Baytril (Heika), if you can give it orally to a cham, I prefer this better. Baytril injections in chams have a few issues. 1) Injection sites may have abscessation which may lead to debridement of the abscesses. 2) There is still debate of whether we need to worry about the portohepatic system filtering out the drug if given incorrectly.(***snakes may be different since their metabolism is slower as well as their digestion of oral medicine.) 3) Injections or oral, just handling the cham stresses it out.
If you have more questions about this subject, don't hesitate to ask.
Matthew