Notes at the bottom were a mistake on our part - you can theoretically customize the screen now to put them at the top but we plan to make that the default behavior going forward (through people who don't like that can of course put them back on the bottom; if you haven't created any notes it won't bother you though).
As far as adding notes to a particular dictionary definition, that's not something on our roadmap at the moment - in theory examples and definitions do have unique IDs, so we could attach notes to those if there was demand for it, but my sense is that what most people want as far as notes is the ability to jot down stuff they learn about words from usage and that makes more sense in its own field than attached to a specific dictionary definition. So I'd rather start with that and consider other places to add notes based on demand.
You could make an example sentence into a flashcard and then add notes to that, but at the moment, they would not show up inline in the dictionary it was from but would only show up when you were looking at that example in its own definition screen. (still, if you turn on "+ for each example" it's pretty easy to get to that screen by tapping on the [+] button; maybe we should consider changing that [+] icon to a little note icon to indicate that an example has usage notes associated with it?)