In my case I've been using bookTome for years to manage my books and my wishlist, I also use Goodreads but I view Goodreads more as a place to add my books and write/read reviews. So I've decided to do the same for the ebooks. Each ebook I add to Calibre I enter it too in bookTome. Well, so far I've only entered though in bookTome the ebooks of the books I already have so I can get rid of the real life books later.
For the other books I've found for free on Amazon and other places (I keep those in another calibre app though since I use the portable one, so I created a directory just for those books), I created in Calibre a shelf called New so I put just a few ebooks there at a time, the ones I find interesting, and I wait to read them to see if they're keeper of not, and if they are I plan to add them in bookTome, and add them in Calibre in the proper shelf.
I've liked the idea of the "To Read" tag so I've added it to the ebooks that are unread in Calibre.