Do you need to have all of the books available at the same time? Initially I put loads on my iPad but then I moved most to a server as I got frustrated by the latest book, usually as a reference, I looked at being placed at the top of the list when books shows all books by their cover. I then use FileBrowser (or they could be on dropbox or icloud) to import more as and when. Just a thought.
You probably know this stuff, but I'll mention it in case other's don't.
In cover view, in any collection except All, you can re-arrainge books by tap-hold-dragging them.
In list view, you can sort by Bookshelf, Title, Author, or Category. Like the cover view, Bookshelf can be re-arrainged. Tap Select, then use the drag handle at the right of the item to drag it up or down. Again, does not work in the All collection. As compensation, the All books list can be sorted by most recent.
Edit: Just noticed that if you are in cover view you can swipe left and right to move between collections. Handy, if you only have a few collections. Not so much if you have a lot of them, like I do.