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I treat my Kindle PaperWhite and Kindle Keyboard the same, which is pretty much the same as my Samsung Tablet and Kindle For PC.
I use Collections to shorten and simplify browsing.
For example, three or more ebooks by the same author, qualify for an author name folder (first name second name). Other ebooks go into a collection that best describes what they are, which might be Collections (novels containing short stories), or Various. I also have one called Non-Fiction. Essentially I am dividing things up, to be more manageable.
One mustn't forget, that entries in these collections, aren't really the ebooks themselves, but the equivalent of a shortcut file on a PC etc. So you can have the one ebook in more than one location. I do that for authors that might co-write with another or who write in the world of another, or if an author I collect has written a short story in a various authors Collection.
I also have distinct differences between my ebooks and devices.
The Samsung Tablet for instance, while containing a good collection of favorites, mostly has ebooks that have some graphic element (i.e colored artwork especially, but not only).
The Kindle Keyboard, my oldest device, I put all sorts of ebooks from various sources on.
The PaperWhite I mostly stick to Kindle Ebooks with. It is also the one I use most.
Kindle For PC I download everything too from Amazon and sometimes others.
When I say everything from Amazon, I have two distinct categories with Amazon. First, there are authors I follow or ebooks I like the sound of enough to pay money for. Then my second category, which is Kindle ebooks I get referred to by BookBub, that Amazon give away for free. The paid for ebooks go to my E-Ink Kindles and if applicable the Samsung Tablet. Whereas as the non collected author freebies, only go to Kindle On PC (until I wish to read them), and are organized into loose Genre collections (i.e. Murder, Mystery or Thriller; SciFi or Fantasy; Westerns or Adventure; etc).
When it comes to keeping tabs on what I have read, I do two things. (1) Leave an ebook I have read at its last page, (2) Enter the dates etc in an Excel file called Readrec.xls, which I have been using since about 1994, which I loosely backdated at that time for all the books I have read since birth, and where everything is listed chronologically. I also enter everything book wise into Booklist.xls, which also keeps a record of when eventually read.
That covers things pretty much, except I go a good deal further, having created a bunch of programs of my own. One program gives me details when I right-click on an ebook in the My Kindle Content folder, it also has its own database and allows me to export, doing all the necessaries, to Calibre.
As much as I love Calibre, and I do, I find it problematical when it comes to browsing and sorting. I have started developing my own program, that works with Calibre, but improves upon the browsing side of things.
But as with all programs, you use them in accordance to their limitations.
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