Bearded Dragon and antibiotics

Question
We bought our son a bearded dragon about a month ago.  He is great his name is Iggy.  He is about 11 inches long now.  Eats well - crickets and greens.  In the past few weeks a strange sore developed on his lower lip.  It was hard and growing for about 2 weeks.  About 4 days ago most of it fell off leaving a raw spot.  The vet said it was mouth rot and gave him antibiotics - Enroflox.  

Because we are new to owning a reptile I am unsure of everything!  (Vets specific knowledge of Bearded Dragons for one!) He has been on the antibiotic for 3 days now.  I put a dropperful in his mouth 2 times a day - he hates it I havae to force open his mouth and shows me his beard when I do this.

I wanted to get a feeling from you if this is the proper approach.  I worry that the antibiotic will mess up his stomach.  He is still eating well at this point.  Is there anything I need to give him to restore the good bacteria in his stomach after we are done?

Thanks

Answer
 I would check and see if this vet is a member of ARAV and if not, find another. And that is only because you are unsure.  Usually Baytril is the antibiotic of choice for mouthrot and most other infections in reptiles.
 Does he have a habit of hitting his tank with his snout?  many a beardie can get a callous on the lower tip from doing this.