Another user that would have a far less enjoyable reading experience without Calibre. I do the same as PeterT with shelves from the series' names that Calibre automatically creates when sending to the reader. I have custom columns added to Calibre for books that I've read.
Once I finish a book, I remove it from the reader and only keep between 200-400 books on the reader at any one time. Having your entire collection on the reader just slows things down, and there's really no need to have them all. Pretty sure that slowdown happens with all readers though, it's not specific to Kobo.
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