William has eye ointment every day and we've got into a routine where I get a treat out, show it to him and say "eye drops". He then jumps on the sofa and lays down while I put the ointment in his eyes. He's not keen but is very patient because he gets his treat straight afterwards. I realise it will be more difficult with a wriggly puppy, but if you can get somebody to help you initially with the aid of a treat and introduce a cue word or words like ears or ear drops, and give her praise and a treat once you've finished she should eventually get more used to it.
I have Thornits at home, although I rarely use it because luckily William and Louis usually have very clean ears, but Wendy's suggestion of a little paintbrush is a good one. You only need to use a very small amount and don't poke it into the ear canal, just gently apply round it.
