Kobokobe are you saying that Calibre's 'Fetch Annotations' doesn't work for your highlights and annontations?
When you plug your device into Calibre you'll find it under:
Send to device
Fetch Annotations (experimental) - it's the last entry
When I've used Fetch Annotations it's been successful - but - they've all been Epubs.
You'll find them in the Metadata section of Calibre - as part of the general book info where you see the synopsis etc of the book.
Not necessarily ideal place to be located but they are able to be amended and copied etc from there.
Let me know how you go and happy travels