HITH is a nutritional deficiency!! The flagellates are a partial underlying cause due to the fish not wanting to eat or not absorbing enough nutrients. Feed foods super enriched with vitamins and you shouldnt have any problems. I supplement all of my food with vitamins to make sure all my discus are getting what they need. If they dont get what they need, then the body starts to break down the cartilidge in the facial region...this creates the holes in the head. Now, some cases of HITH has puss coming out of them. A secondary bacterial infection is VERY common and is very treatable if the tank is kept pristine and actions are takin early. A common antibiotic should help. Metronidazole is a common med to treat for flagellates, but it works best when given to the fish in food since most metro you find is glucose (sugar) based and if given to them in food, it will go directly into the bloodstream....making it more effective. You can treat in the water, but Dimetronidazole is MUCH more effective and is designed to dissolve in the water, unlike normal Metronidazole.
-Ryan