Will you PLEASE help my Betta fish?

I have a juvenile betta fish. His name is "Dewey". I put him in an aquarium called "Eclipse System 6" by Marineland. I noticed he has fin and tail rot. I have added medication for the disease along with aquarium salt. I have followed all different kinds of help, but his caudal fin doesn’t look any better. I keep him really clean, maybe too clean. I was wondering if that tube in the tank which sucks up the water, was tearing up his fins. " Dewey" seems to swim around it at times and his fin gets pulled or sucked in and he sometimes struggles to remove it. I was wondering if he would be alright in a 2 gallon fish bowl with a heater. Oh, he does eat and is very active too. PLEASE HELP!!!! Your answers are greatly appreciated. THANK YOU!!!!