D.W.
Two ways have worked for us.
#1. Do it while he is sleeping...for us works 95% of the time.
#2. Lay him on the floor, you sit up by his head, with his head between your knees (your knees by his ears). With you being behind him, he will be looking up towards you and it's easier to drop them in. Also, be sure you aren't touching the bottle to his eye...that will contaminate the container and my be why it isn't going away.
bty...I have to clip finger and toe nails while my son sleeps. Otherwise it's a total battle.