So I think Im an idiot, or just missing something obvious. I have a set of books, I can send them to my Kindle Fire, I can see them in the file viewer, but they are not in the kindle app.

What am I doing wrong?
If you have created an epub, you can mail it to your tablet. If it's the first time you've done this, you'll have to confirm your email addy. (The address of your tablet can be found by going to Content and Devices on the Amazon store. You can change it to something easily remembered.)