Get an Evernote paid account and you can upload up to 200mb per note. This will cover most text only books and many short and mid length books with graphics. For PDF's larger than 200mb, you will have to split them. Once in Evernote you can annotate, flag, and add notes to your hearts content and you will be completely platform independent. I do this with Android and Windows, but it will work the same with iOS and Mac. A great part of doing this in Evernote is the whole text will be searchable from within EN so you will not even have to remember what book you saw something in to find it.
To get started, I had to go into the Evernote mobile app and sign up for an account. It only costs 1¢ per month for 30 days of storage (which I have used), and if you use more than 50 notes you can get a credit too. Once I had my account set up, I opened my first note. This was the notes list, and it was incredibly beautiful. But, because it is a note list, it had no category or tagging system. It didn't look right, so I put it into a folder and tagged it. Then I created a new note named “Funny Book”, and inside it I created a new tag, then added the note to its folder to make it easier to find. Then I went into my folder of notes and I added “Funny Book” to the Favorites, so it's the default folder. When I want.