If you use calibre as the main location for all your books and collections info, etc, you can have it send books to your devices.
Both will allow you to create a custom column in calibre that contains collections and sync those collections. They will cost $2.99 each I believe.
- On your computer, calibre can also natively read pretty much any ebook format in its own ebook-viewer.exe (or you can set it to open in the computer's default app).
- For the Paperwhite, if you want to manage collections other than through the Kindle itself, which is slow and bulky, you will need to jailbreak it and install a kindlet app. If you're interested, start reading here: https://www.mobileread.com/forums/sho...d.php?t=186305
If you do manage to restore your collections within the Kindle app, and import it to your Paperwhite, then the same Paperwhite hack will also allow you to export the collections to calibre. But you may not want to bother, as it means your problem is already solved.
Notes, highlights, progress, etc. will always be associated specifically with the app that opened the book, regardless of anything else. Within an ecosystem, Marvin can sync between multiple instances on different devices, as the Kindles/apps do via Amazon's servers, and calibre within its highly portable database.
I hope this helps you, or at least gives you some good ideas, but if you need any help, just ask here -- MobileRead is full of helpful people who can probably answer any question you have!
And on that note, welcome to MobileRead!