One of the problems with ear cleaning is that it can be unpleasant from the dog's point of view, and it's actually very easy to hurt them. And if it hurts once (especially early on in his ear cleaning career), the dog expects it to hurt again - so naturally, avoids it like the plague.
I'd suggest that you take the process quite slowly. That is, first teach the dog that having his ears handled is no big deal, and comes with the bonus of lots of treats and general "good things". Don't even try to clean at this point, or get anything inside his ear. Just sit and fiddle with his ears, giving him lots of praise and treats. You might try massaging them even - most dogs enjoy that. If you can position yourselves so that you're sitting on a chair and he's sitting between your knees with his back to you, you'll find this easy (and you'll have a reasonable amount of control of the dog also). Do this daily, preferably when he's calm and quiet, even a bit sleepy (that is, relaxed).
Once he's accepting of the ear massage (preferably enjoying it, but at least accepting it), then move on fiddling more obtrusively - turn his ears inside out periodically, before returning to massage. And when that's no big deal to him, step it up one further - bring the ear cleaner with you. If that makes him suspicious to he tries to run away, don't do anything with the ear cleaner for a while. Just let it sit there, whilst you continue massaging and generally fiddling with the ears, giving praise and treats now and again (e.g. after each time he lets you turn his ears inside out).
And once he's relaxed and happy once again, try a bit of light cleaning. Do NOT try to get inside the ear. Just take your cotton ball, or whatever you're using, and clean the inside of the ear flap lightly. Then return to the massage thing (especially if he's enjoying this part by now). From there, you can just slowly work your way toward a full cleaning. Don't go further than he's comfortable with - try to keep it all positive and a generally pleasant experience. It may take some time, but eventually you should get to the point of being able to handle his ears without great fuss (which beats spending the rest of his life battling over ears).