I have a gelding who apparently has an allergy. He is itchy and has rough scaly patches under his belly. The hair in his ears is thin and patchy. I don't notice him rubbing a lot but he obviously does. He stays up during the day, out at night. Flies and sunlight are not a big issue. Any tips on the best way to determine the cause and find a treatment? 

your vet can do a blood allergy test and that will be the most accurate. If you didn't want to do that start elimination diet but this will take a long time. 

First question: Is it seasonal? Summer? Spring? 
I can almost guarantee it's some type of gnat. 

Sounds like sweet itch. My horses are covered ear to tail with belly band fly sheets/neck covers and still get them on the under belly all summer long. They're caused by insects. The E3 Medicated Wound Cream works super well, I can get it to go away within a couple days. And just fly spray them daily. I got EcoVet fly spray, it might choke you out but when I spray a horse there isn't a fly to be seen in the barn for hours after. It's ridiculously strong. So I started spraying the horses with that where the sheets don't cover, so far they haven't come back yet