When you're on manga's main page or chapter you need to click on icon next to login button, that now is your username and you can select to read, read, favorites and subscribed from it. Favoriting main page favorites entire series, favoriting chapter only favorites that particular chapter. One-shots works like chapters. You can mange those in Lists.
Yes! Thank you so much. I kept having to make a notepad to keep track of manga. This is so much easier!