Now you see why Sony buyers are willing to pay more for a Sony reader.
I have my books organized in to various collections. If the book is in a series, there is a collection for the series, and the books show up in the series order.
If the book is also in a sub series of that series, it will show up in a collection named for the sub series, also in sub series order. As well as being in the main series in series order.
Most of my books also show up in collections based on the authors name. Depending on the author and other considerations, the books in the Author's Name collection will appear in order of publication or grouped as series with the books in series order. I usea custom series like column for this, rather than the actual authro column in Calibre.
I cannot imagine trying to deal with over 1000 books without a way of grouping them into collections.