Fountain drinking
If Bobbers really likes to drink out of a bowl, I think this is okay. I usually encourage any way of getting an animal to drink more.
This should not take the place of appropriate misting or humidity as his/her skin and eyes require more than just oral hydration. You should also be aware that many chams like to poop in their standing water. If the water is not changed soon after this event, bacteria will quickly grow in the warm, humid environment you have. Drinking soiled water is setting yourself up for problems.
That being said, if you are cleaning daily, this does not have to be a problem. (Most people (including myself) do not have time to be washing out a fountain every day, so most keepers won't bother.) I probably would recommend giving Bobbers a water bowl for 10-15 minutes for him to come down and drink, and then remove the water bowl or fountain so he can't defecate in it.
If you chose to continue using your fountain, I suggest running it (outside of the cham cage) with a 10% bleach solution for about 10-15 minutes and scrubbing the surfaces well. After this you will run the pump and rinse with regular water again and again until you cannot smell any bleach. If you smell anything you need to rinse again. (Like I said, a real pain.)
I'm not into anthropomorphising, but I do believe that animals do have preferences and if Bobbers has come to like to drink when you offer him standing water, so be it. He doesn't have to live in the wild, so his modified behaviour should not be detrimental.
Personally, I have a panther cham. He doesn't like to drink out of a bowl. My crested geckos do and I have an exoterra fountain that I don't use anymore because of the mess they were constantly making in it. Much easier to use a bowl.
Summary- If you can't keep it clean, don't do it.
Matthew