re: "... is there a way to "mark" a page or specific paragraph ..."
Yes. Can set/clear unlimited number of book marks. Can highlight a section. A list of bookmarks and highlights let you jump to any. There is a keyboard and you can enter annotations that save and key to the text. All are a tad clunky. Making notes is a lot like taking notes using your cell-phone. The UI for viewing and jumping to bookmarks or highlights is much harder than the "flags" mentioned. On the other hand, I can highlight a term and jump out to wikipedia to lookup more detail, or lookup a term in a dictionary