Sinus headaches are the result of swelling, inflammation or infection in one or some of the sinuses in your head. Many sinus headaches exhibit the same symptoms as tension headaches or migraines, but often have additional symptoms such as congestion, cough, sore throat, fatigue, or nasal discharge. They can be triggered by allergies, pressure changes in the ear, tooth infection, a cold, a bacterial sinus infection, or sinusitis.  While it is important to consult your doctor to accurately diagnose the type of headache you are experiencing, there are a number of different ways you can treat a sinus headache using both medical and home remedies. In general, most sinus headaches and swelling are gone within four to eight weeks with or without medical treatment. 
Sorry to hear about your son’s struggles. It sounds like you’re doing all the right things. For kids with chronic rhinitis and chronic cough, I am suspicious of reflux (GER/GERD) as a contributing factor. Take a look at the articles on this site for that topic. Regarding the precise amount of Manuka honey to use, it ends up being about a tablespoon for an 8-oz bottle of saline. Manuka honey may help reduce inflammation, studies have found that Manuka contains both a strong anti-microbial, and strong anti-inflammatory agents … worth a try.
Please let us know how it goes, and thanks for visiting.