In all honesty, you may not notice vast improvement for up to a week AFTER you finish administering the medication. Definitely make sure you take him/her in for the re-check with the vet just to be sure that he is improving. Full recovery can take weeks. :/ Very frustrating. But hopefully you will notice slight improvement after the first few injections. Depends on the animal and his/her response to the medication.

Did you have a tracheal flush done to identify the exact strain of pathogen? Or did the vet just give you Baytril?