I use calibre to manage my books and use custom columns.
My method is a bit of a pain and got more complicated with the T1 where you have to go to the book list to delete books.
I have a custom column for each reader which is a Y/N column.
Another Y/N for Read and one for TBR
And a text column for my comments which mostly contains page numbers of books not finished.
When I plug in a reader I sort on the reader column. 350,600 or T1. I mark any books that are deleted (ie in custom reader column, but not on device) as read.
Then I then bulk select all the books on the device and mark the reader column.
With the T1 I also mark page number that I am at in unfinished books in the my comments column. Not necessary for the 350 and 600 as they always seem to keep their page. My T1 has lost them
twice.
Anyway it is as I said a pain in the butt, but I read a book or 2 a day in the winter and lose track of where I am in a collection as I regularly read on 2 different readers.
Oh well at least I don't have a thousand physical books to deal with
Helen