ID 00.00 is the ID you would give to your JDex, wherever you might have it. If you have your JDex in, say, Apple Notes or whatever note app came with your phone, you’d keep that folder on your filesystem empty and just consider that app to be 00.00. If you’re using something like Bear or Obsidian, however, where notes are actual text files on your filesystem, you’d store them in the 00.00 folder. (Although you don’t necessarily have to! I think some people prefer to store JDex entries in the actual folders they represent.)
The JDex is meant to be a master record of your entire JD system. Every area, category, and ID that exists must have a JDex entry. And since the JDex has an ID of 00.00, it also has to have an entry within the JDex. It’s not an infinite recursion thing; it’s just an empty note titled 00.00 JDex as a way of saying “hey, this ID is taken”.
Each area and category also has room for a JDex at X0.00. I have not had to create an entirely new JDex for one area (nor do I see why you would want to), but for the customized college area in my JD system, I documented how I designed it in the 20.00 entry in my JDex. One advantage of a JDex entry is that you can document extra notes and info about a specific area, and if you expanded an area like I did, you should write down exactly how you did it in the X0.00 entry.
I get that my explanation might be a bit unclear, so feel free to ask clarifying questions! I and everyone else on this forum are happy to help you out.