I have never found a better way I'm afarid but lying them on their back straddling them with their arms to their sides and your knees either side of their head keeps their head still and our hands free
use one hand to open lid, drops in and chocolate to be administered too sweet
Not the answer to your question but one really good tip that I've found when our DS has conjunctivitis is to smear his eyelashes and lids with a bit of vaseline before going to bed/nap. It means that his eyelids don't stick shut whilst he's sleeping (always really upsets him). It also makes all of the gunk much easier to wipe off once they're awake. I checked with my optometrist and he said that it won't do any damage to his eyes.
Good luck with the drops, I agree that a sweet reward seems like a good plan.
Did you know that when the drops go in they go down your throat and taste really bitter? DD had conjunctivitis and the first day she was fine and then she wouldn't let me put them in. Then I got it and realised what happens. It's really unpleasant so I would suggest a drink straight away to wash away the taste. Don't know about actually getting them in though! I just resorted to squirting loads round her eyes and hoping some went in!