Teaching your dog to willingly accept her ears being handled will pay dividends - whether you need to medicate her ears with drops or just keep them clean.
Instead of tending to the bottle only when its time to apply medicated drops or ear wash, make a point to handle the bottle multiple times per day. Set the drops on the counter and toss your dog several small treats. She might be suspicious and ignore the treats at first. Thats fine. Act like you didnt notice and busy yourself in the kitchen, ignoring both the medication bottle and your dog.