Jim,
Welcome to the Scrivener club!
[size=140]Notes[/size]
As a writing tool, there are so many ways to take down notes it is difficult to list them all. One could write a thousand words just on the topic of chapter notes, let alone all of the other kinds of notes. 
Here is a basic summary of the types you have available though:
Project Notes
Same general idea as document notes, you write them into the inspector as well by toggling the notes panel to project mode. The big difference here is that project notes are always visible from any inspector pane. They aren’t attached to anything in the binder at all, and so are best for big ideas, to-do lists, and that sort of thing.
Documents
As you’ve already been using as a matter of fact. Either as fully fleshed out binder items with thousands of words in the main text editor, chock full of meta-data in the Inspector, binding them to actual pieces of the book through relations between that meta-data, or just simple paragraphs or bullet notes on the synopsis of the index card, and everything in between. The binder item is the most useful chunk of data in the project, and has a large number of features and techniques available to it.
Document Notes
A component of documents themselves are their note fields in the Inspector. These are useful because they keep the binder tidy, and keep notes relevant to the pieces of the book they pertain to. If you have a note that doesn’t pertain to a piece of the book yet, then you can create an empty document and add your notes to the Document Notes field. Briefly summarise the idea in the synopsis and file the card away in a folder for “I don’t know where yet” bits. Documents notes have one really great visibility feature, and that is the fact that the inspector shows them when you have done only so little as select the card in a corkboard. This means less navigational clicking. All you need to do is click on a card to read its detailed notes. With a split view, that means you can read detailed notes from a corkboard collection of them in one split, while working on the book manuscript in another split.
Note that you can interleave note documents with manuscript documents right in the book outline if you wish. A lot of people like this technique because it blends well with Scrivenings mode; you can see notes and book text all together in the editor. The secret ingredient here is the “Include in Compile” checkbox in the inspector. Turn that off and the entire document becomes invisible to the final output.
Inline Annotations
This is for your very contextual notes. Stuff that you wish to remark upon for a precise piece of prose, or a paragraph or two. They are made directly into the editor and stand out from the normal text as being highlighted in red and surrounded by an outline. They are your red pen margin notes.
[size=140]E-book Finishing[/size]
I would say, only in special cases. Scrivener is capable of quite a bit all by itself, and produces what will be a polished and professionally put together e-book. A full table of contents, hyperlinked to the sections, linked and back-linked footnotes, graphic cover, et cetera. You might need a finishing tool if you wish to do custom CSS, or any global embellishments like a graphical scene separator, that sort of thing. Sigil is a very nice tool for this, and you can get to .mobi from that if you need, using Calibre or KindleGen.
