My 3 year old son as a horrible cough and is very congested. He has finished 2 BOTTLES of cough and congestion medicine and isn't getting better and actually sounds worst. What should I do? He is also running a fever most of the time.

How many days?
Those cough medicines are only an adjunct to the usual: keep him super warm, rested but at least partly sitting up, humidifier going, lots of lukewarm weak liquids like broth and juices, and children's tylenol.
THEN you call his pediatrician, in case of something like whooping cough.