I don't have any relationships set to the products table. I have the sub category going to the main category. When I insert a product I have a drop down box and I select the main category. I do have a column in the table for sub category, but nothing inserting into it yet.
So I insert a product into main category jewelry. It gets a categoryID of 2. Then I went and created a sub category earrings set to main category jewelry. Then yes, the region says it is in all main categories (which I believe is just because it is returning all values in the category menu). But in database it only has a relational category id of 2, which goes to jewelry so it is correct.
(side rant below)
I looked past the repeat region and tried to get the navigation to show a dynamic nested menu, but it wasn't working. What was happening was I have a template with a require for 2 menus. One is the main navigation , and one is an admin navigation. I clicked to change the menu (delete the dynamic menu items) and hit finish. Then it said my template page needed saved, even though I didn't notice any difference at all. I figured it would change it in the php page so I opened up the menu and nothing changed. Uploaded it anyways and got errors galore! My mind is wound up and I guess I am not thinking straight because no matter what I do, it doesn't work. I even deleted the page and re made it.
I have been working on this all day just trying to get familiar with everything and every turn makes something else not work.