I don’t think there is a standard protocol for prompt book set. As long as your book has all the info needed for the show, and is organized in some fashion, do whatever makes the most sense for you.
I do put my script at the back of my prompt book because I have a pouch of pencils, etc at the front of my binder, and papers lying right on the pouch are too lumpy to write on. Also the first and last tabs in a binder are the easiest to grab quickly, and since I like the contact sheet & schedule in the front, I’d rather have the script at the back than somewhere in the middle. Finally, it’s nice to have a quick visual of how many pages are left, and that’s hard to see with other tabs after the script.