It sure isn't easy.. Cheno has ERU and last summer he got a fungal infection which led to lots and lots of medicating.
All I can say is to try lots of different configurations with how you hold his head. I like to get right up against the head so if they swing it I go with rather than getting whacked, etc. I have used the head over my my shoulder, which works sometimes. Rest your arm and heel of your hand against him so you move with him, hold his head steady with the other hand, arm over his head. Big PITA isn't it? Having someone hold your horse and give him a tasty tidbit may help with keeping him occupied but it rarely worked for me.
Practice a bit without the medication first.