Taken once or twice a day, amitriptyline is very effective. I have had no problems with my eyes at all. It’s really not necessary to give him eye drops for more than two days — they don’t do anything good then anyway. (I’m guessing that the vet has recommended longer periods because you’re worried about scarring.) You can try using one drop in each eye every day until they are gone or you are sure they are gone, whichever comes first — but be careful to follow directions so as not too dilute the medication!
You may need an appointment with your veterinarian if his condition doesn’t improve within a couple of weeks after starting treatment. Good luck!