I would like to give some experienced advice about notes and bookmarks.
Short answer: don't use the app you are using to read. Use other services like Evernote/OneNote, or Apple Notes, or whatever.
Long answer: I like a lot this program but it lacks two very important things (for me, of course): no iPhone app and position sync is done manually.
The last one is an absolute no-go. ¿Why? Because if I forgot to manually sync the position (that happens almost always), when I go to my other devices, they are not synced. That is the reason I commented before that at least sync position must be automatic, at least when closing the book/app.
(Other collateral thing in relation to manual sync, that is covered by the book "Why software sucks?" by David Platt, is the list of actions to do before and after sync: to do the sync it asks *twice* after selecting the option. Oh, man, I had the will to press a button. Do it, and if I've mistaken, give me an "undo" button. Please, please, do a usability study. People usually is not stupid).
Sorry for the interruption. If I don't write it I will die of disease.
Why don't use the app annotation system? Because the problems currently in discussion. Nothing lasts forever, and apps less. You are comfortable using Marvin/BookMaster/uRead/Whatever and suddenly discover other better application, or your current app developer finds the love and stops making apps, or you get tired of iOS/Android/Windows and want to switch (perhaps other day I will talk about the Golden Jail with Pixie Dust).
Then you will discover you have read a zillion books with X app, another Zillion of bookmarks in Safari, have two zillions and half of notes and a scrapbook in Whatever app of about three thousand terabytes of data... And cannot change because that.
(As a side effect: don't use the app for your book repository. The reasons to not do this are the same explained here).
Please, don't enter in the Golden Jail with Pixie Dust.
What I do? In relation to books, I export my notes to Evernote. Doesn't matter if I'm reading in BookMaster (not since it lost the position of one of my books), Marvin, Hyphen, iBooks or Kindle (eInk and Apps). If I'm reading in an app, I directly export the annotation. If I'm reading with my Kindle Voyage, once read the book, I open the annotation text file copy and paste into an Evernote note.
Now I have a lot of little notes in Evernote. I can select all for the book I've read, merge into one big note and move to my "Reading Notes" Notebook, even with keywords. Muy notes are all in the same place, keyworded, with the same format and never will be lost.
When reading old dead tree books (btw I *still* read a lot of these) I used to annotate them with pencil and sometimes with color pencils (each time you write with a ballpen in a book, God kills a little kitten) . Now I take a photo of the part of the page, reference and annotate it and send to... Yes: Evernote.
I use Evernote, but you can use whatever application you want. But insert in your mind the phrase "never in the Golden Jail with Pixie Dust": have a path to recover your notes in a more or less standard format. Evernote exports to standard XML format. My scrapbook is GoodNotes that syncs across devices and can export to standard vector PDF. My PDF reading tool is GoodReader, that uses the standard PDF annotation system and can maintain a synced list of files with a server...
I'm not recommending apps here, I'm telling you the ones I use that have a big "Golden Jail with Pixie Dust Exit Door".