I am not sure how kindlean works, has an asterisk besides the paperwhite on their site saying it requires use of their ebook agent or something to that effect. Not sure what is entailed or what extra steps they require.
I did my collections on PW manually as I was transferring all files over from my kindle 4 Very time consuming to do it though the manager on the PW. If I was doing 10 at a time over a period of months, it wouldn't be so bad. I store my books locally as I have very few purchased. I put them in collections stored by author name and I know who I want to read so I am able to go to that author and pick a title which intrigues me at the moment.
It is also a slow process doing it a batch at a time the way I just finished doing. Send to device... wait till it's finished, unplug device ... wait until it indexes .. make collection name, cycle through pages checking off books and waiting for it to refresh after each page. Back to send the next batch.....
I didn't feel comfortable with hacking my unit just yet as I haven't had it long. Just in case there is something wrong with the unit I would like to be able to send it back under warranty.