backup early. backup often. You should backup your mac book. Apple's iCloud service is for sharing your files among your devices. It's not for backup. When you delete an app, all the files used in the app are deleted too. You have to have them in some other location to get them back.
GoodReader
-- With GoodReader on your iPad/iPhone, you can read virtually anything, anywhere: books, movies, maps, pictures.
-- sync with Dropbox, OneDrive, SugarSync and any WebDAV, AFP, SMB, FTP or SFTP server
-- The types of annotations that can be created and edited in GoodReader include typewriter text boxes, popup comments ("sticky notes"), text highlights, freehand drawings, lines, arrows, rectangles, ovals, cloudy shapes, text underlines, strikeouts, text insertion marks.
http://www.goodiware.com
Has a good reputation, but I haven't paid for it.