Cruzan80: I'm not sure what problems you are having with the set-up. Most of the options in the utilities plugin work by selecting a set of books, choose the options and let it go. The reading position storing does need some set-up of the custom columns. If you describe a particular problem or function you want to use, then I can help with that.
But as you mention the shelves/collections...
Kobo changed from "Shelf' to "Collection" as of firmware 2.9.0. All the devices using the current firmware use "Collection". I haven't updated the word in the plugin partly because I've been lazy, and partly because I preferred "Shelf". "Collection" is probably the better word. Also, as there are still a lot of people using the older firmware, it isn't an urgent change.
To set-up the shelves/collections from calibre, see
https://www.mobileread.com/forums/sho...d.php?t=193184. The first post is a good description of how to do it. And there is lots of discussion and some interesting ideas on other shelf types in the thread.
For the series ordering, once you have collections that are named for the series, it is easy. The "Order Series Shelves" option does it automatically.