1. Sorry, but your request is a bit unclear. Do you want to remove the subcategories from the last menu item and add them to the second one?
2. Concerning the portfolio categories, you need select “Categories” in Screen Options as shown on screenshot, in Appearance > Menus. After that you’ll see the categories block on the left side.
One standard license is valid only for 1 project. Running multiple projects on a single license is a copyright violation.