When I bought my paperwhite, registered it to my account and then did my first sync (using wifi - 3G will not work) I could see all my Collections from my original devices with the following Configuration on the Home page:
All (highlighted) | Downloaded ___ Collections ___ Title
and all I had to do was long press on each individual Collection name and from the menu that popped up select add it to my Home page or download (I forget the exact wording). This was for the 1st Paperwhite and I'm not sure if it has changed since then. However, since I stupidly deleted some of them, I had to recreate quite a few and found it far easier to recreate them on the Paperwhite than on older Kindles;
a screen comes up with all items sorted by (your choice) Author, Title or Recent) and you simply scroll through them and tick the boxes in front of the ones you want in the Collection. I did this with my two Kindles side by side.
then tap on the Done button
I was able to sort out around 1300 books in the space of two hour TV dramas during commercials. Keep in mind that books can be in more than one Collection, so you don't have to slot a book into just one. I have several in 3 collections: The Complete Morgaine is in Cherryh, Old (books I have previously read in another format) and Read _SciFi_ Fantasy
as for mobi files, their Collection presence totally depends on whether or not you have transferred the mobi books through your Amazon account. If not, Amazon has no record of them and thus does not store their Collection tags. I transfer all my mobi files (around 200) through my account for that reason
You can import the collections from a specific device.
But that is only the list of collections and the links to the books associated with the collections, NOT the books themselves. Confusing.
- If the books are present on device2, when you import the collection from device1, the books are then put into the collections.
- If the books are NOT on device2, it will NOT import/download books in the collection.
Cloud collections are different from the local collections on Kindle-for-PC and Kindle-for-Mac, as the collections can be managed globally. But using cloud collections is not as easy as collections on Kindle-for-PC. The web app is still rather clumsy and does not work well with large number of collections.