As others have suggested or hinted at, it is really worth getting a bike fitting. By switching to clipless pedals and shoes alone, your saddle height will / should probably change. If you’re dropping your ankle, it could be that your saddle is too low, or that it’s too far back or forward. There are some bike fittings that are more expensive (~$200 or even more), and these can be super helpful. You can also try having a friend help, or even video yourself and post it for critique or feedback.
In my experience, foot placement is something that you can adapt to somewhat, though I tend to think that what feels naturally efficient can often point you in the right direction – or at least to a starting point. One benefits of a good fitting is that they may find that you’re more efficient in a certain position – sometimes much stronger (they can “discover watts” by changing your position).
I myself have somewhat large feet for my height and am a runner, so I began by putting my cleats further forward on my shoe. (I also was told, when I first got into biking and got my first “real fit,” that dropping my heel was a good thing, so with a longer foot-as-lever, I thought it would make sense to put my cleats forward). I have since moved them back, and don’t mind occasionally playing around with cleat position. I think it’s something that you can get used to, as long as you make small, incremental changes, AND as long as you don’t over-think or obsess over the position of the cleats. It can also help to have data, such as power data or – more likely – comparing how slightly different positions feel in a series of short time trials or loops. It’s important that one is able to relax the muscles that don’t need to be tense at a given time in order to be efficient, and to not force the body into something that feels painful or wrong, since the cycling motion is one that will involve thousands of rotations per ride. (There have been cases of elite runners getting coached to land on their feet differently, even after years of running in their “natural” way, even if their “ugly” or “theoretically inefficient” running style still got them to a world-class level. These attempts to change their running gait seem to usually go very badly, resulting in injuries etc.).
I would also spend some times on YouTube hearing from different coaches and fitters. There are some really knowledgeable guys on YouTube, along with coaches who look at and compare different studies. I have found it’s best to listen to a variety of opinions just so you can hear what’s out there. There are also some great articles about this on Slowtwitch.com – along with another good forum (mostly triathletes, but also lot of bike knowledge, and people who know a lot about bike fit).
