How can i mark books (pdf) in iBooks on my iPad?

Hello,
I am using the new update - and Mavericks on my Macbook. I want to synchronize those marks and annotations, but i don't know how to make an annotation or marks in iBooks on my iPad -
please help! thank you!

I've been looking at this today also, unfortunately it looks like there is no option in iBooks either in Mavericks or iOS to annotate and sync those notes via iCloud, when the book is in PDF format (despite the implication that you can). Best I have found, is that bookmarks sync between iOS devices, but not to Mavericks.
The annotation option is not present in iOS, and the PDF just opens in Preview in Mavericks, rather than iBooks.
I found this workaround helped:
1) Convert the PDF to ePub format - you can easily do this here for free: http://ebook.online-convert.com/convert-to-epub
2) Add the converted ePub book to iBooks on Mavericks. (Add to Library from the File menu)
3) Sync the book to iOS using iTunes in the normal way (the ePub book will automatically appear under Books in iTunes)
4) You can now annotate by selecting the text in the book (in either Mavericks or iOS) and these changes push via iCloud provided this is all setup normally. In iBooks on Mavericks, you may need to Authorise the computer.
5) Then to annotate In iOS, highlight the text, the popup menu gives the option to add notes.
Hope this helps

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