I take it that you are going anti-calibre route
Because Kobo Utilities-extended edition does all the heavy configuration.
You just set that, the send books
The Kobo device driver (also configured) takes care of Series (no side steps like needed for a Kindle).
I believe Shelves was renamed Collections. (I don't use) You can configure that to use a variety of ways. Some use a Custom (tags-like) column in calibre as that source.
Do Note: You must do a Second connection for these to take place (all you need to do is wait for the jobs spinner to stop). Kobo absorbs the book into its DB on the first disconnect (do wait for 'Processing' to complete), Now there is a place to log those collections and series to upon the second.