I have "To Read" and "Read" tags in Calibre. When I start a new book, I mark it as "Currently Reading" on Goodreads. When I finish it I:
1. delete it from my ereader (I only keep "To Read" books on my ereader).
2. update the status on Goodreads, give it a rating, and possibly a review.
3. change the "To Read" tag in Calibre to "Read".
My TBR books are more a pile than a list; when I finish a book I poke through my ereader to decide what to read next.