I'm sure a lot of people here have been through this. I can say I have once. My male must have somehow pierced his elbow on a dead plant twig (that was the only thing sharp I could find in the cage) and by the time I noticed it, it was very infected. The vet said she could even see bone, she said that the infection had most likely spread and she wasn't sure if he was going to make it. She gave him an injection and then I had to give him a baytril (I believe) suspension orally. The funny thing is, during all of this he never stopped eating or drinking and never looked sick...his elbow just looked really bad. Injections are great because they start working much faster...straight into the blood stream rather than having to be ingested and absorbed. But long story short, my male is %100 better and only has a little scar to show for it and he is still kicking over 3 years later But if you are worried, don't be, injections are quite common in the reptile world.
Not for a URI but hermie routinely has to have injectable antibiotics for his kidney infections.
They're pretty quick and simple -- easy to do at home if you have to. They should just be going under the skin ... usually around their shoulders is a good place because there's some extra skin, although the volume given is usually pretty small.