Want to just make sure I got it right: When I click on KEYWORDS and the cool black thingy appears, this is just a “holding place” for ALL the keywords in that particular document. They may or may not be assigned, they are just in a holding space. I then need to click on the key (keywords) on the bottom right to insert them. Now aside from the keyword itself, which can be edited under the “key” option in inspector, making it a child or parent and the color, that can only be done in the HUD right?
Yes, you have it all right. 
thanks… for a while, i was just seeing the words on the black HUD and could not figure out why they were not being assigned… i could not understand why they were “universal” across the whole project… and i was with the tutorial the whole time… sometimes you just dont pay close attention and pay dearly for it.
The only places that show assignment are those places which are in direct relation to the item itself. Scrivener is pretty strict about the notion of not tying info windows to things in other windows, except where it must for Mac conventions (like the colour palette). So there isn’t a mysterious floating info window that shows selection details on an item—rather that info is embedded right into the same window in the Inspector, or in the info split in QuickReference panels. Keyword assignment can also be seen in the Outliner and, more symbolically, on the Corkboard, if you turn on the respective meta-data options for those in the View menu. The Project Keywords window shows every keyword you’ve ever made and left assigned to something, even if you’ve since removed all assignments to it. It also serves as a place where you can organise them into groups and change their names and colours universally. It is also a useful tool for assigning groups of keywords to groups of items, so anyone dealing in lots of keywords and using them as a part of their workflow would do well to learn it.
So yeah, rule of thumb, if it is floating in a window, it relates to the project in some way.