Syncing notes, highlights, and bookmarks between iOS devices

Hi,
I've decided to digitize my technical library by purchasing ebooks from now on. The problem is which ebook format to go with. My ideal requirements would be to be able to purchase books from various sources and be able to read them both on my Mac and on iOS devices. Additionally, I want to be able to sync the highlights, bookmarks, and notes among all of these devices.
Currently, the real winner that satisfy all of these conditions is Amazon mobi format. The only problem is that I can only purchase books from Amazon if you go with this platform.
On the other hand, Apple iBooks is a close second here - the lack of a solution for a Mac is a problem, but I am hoping that Apple is working on the iBooks application for the Mac. The syncking of notes, highlights, and bookmarks among various iOS devices is a nice feature, and it does not require a tethered connection to iTunes - instead, these items they can now sync wirelessly among devices on the same iTunes account.
My question is if the syncing of notes, highlights, and bookmarks works only with ePub books purchased from the Apple's iBooks store or if this feature works with unprotected ePub books purchased elsewhere and loaded on iOS devices via the iTunes syncing feature. For example, most of the technical books I am going to be digitizing are Cisco books published by Cisco Press. As of late, most of their ebooks are available in the unprotected ePub format, and I would be using the iBooks app to read these books. So, if I were to purchase ebooks from Cisco Press, would I be able to to make a note in a book on one iOS device (e.g. iPad), and later see this note in the same book on my iPhone?
Thanks!

This page http://support.apple.com/kb/HT4059 says (I havn't tried it though) :
iBooks will automatically remember where you left off each time you close a book or return to your Home screen. Tap the bookmark icon in the upper-right corner to bookmark a specific page. Wirelessly sync your Bookmarks, Highlights, and Notes with your other devices using your iTunes Store account by tapping Settings > iBooks > Sync Bookmarks > ON.

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Message was edited by: applerock9999

Thanks so much for your detailed reply. Much appreciated!
Just to confirm my understanding that 100% clear on the solution, if my wife gets her own iCloud account, on her phone she'll receive her own emails & iMessages (makes sense) but not contacts. Calendars though we could share.
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Syncing notes, highlights, and bookmarks between iOS devices

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