Before anything else, talk with whomever is going to be printing and doing the die cutting. They will tell you the page sizes you are going to need, which all depends their die cutting. They will/should give you dimensions for the tabs but will also make the dies work with what you need to have on those tabs. They will also tell you how much clear area at the spine they require.
After that it is fairly straight forward. You will simply set the page size as required, with the margins needed. Your thumb tab positions are in part going to depend on the amount of verbiage you require for them. And you will likely make adjustments as you go. I set up master pages for each section with the "tabs" (really just a text frame that's rotated) positioned appropriately. I add the text in them, but you can also use variables if desired. I generally don't.
That's about it off the top of my head. I'm certain I've left a bit off. All of the set up dimensions come from the people doing the printing and die cutting. Communication with them is everything. It's part of what y'all are paying them for.
Thanks so much for getting back to me about this, I'll get in touch with the company and see what sizes/measurements I require.