Indie's had eyedrops twice now. We waited until she was calm (not racing round the garden or on 'alert' in the house- normally just lying down etc. then we'd give her treats as we approached and sat down. Two man job- one to hold her gently but firmly whilst praising and one to prise her eye back gently and quick-drop! It is frustrating though as she often moved at the important moment- or the dropper didn't drop quick enough! make sure the drops are right at the top of the tube ready to come out with little squeeze so when you do get him in position it's over quickly.
Possibly, if he's really uncomfortable with it, just let him sniff it whilst it's not doing anything with him- 'introduce' it as it were, and praise etc so he gets used to the smell being a lovely thing. Then just do one eye at a time, let him rest, have a play, and go back to it when he's once again calm.
we had ear drops with our last cocker when she was tiny, i don't remember her having any issues (and i was only 7 so watched- no ear dropping for me!) so i can't advise on that!
