Hi, Brian, and welcome to Accordance! Lets talk about each item:
1) Our notes system is highly flexible, but admittedly a bit odd to get started in. We're probably going to do a nice revamp of it soon, but in the meantime! User notes are organized in files. Each file can have as many or as few notes throughout the Bible. So, you could have a single file spanning everything, or a 'Teaching Notes' vs. 'Study Notes', or a dedicated one on Ephesians - its up to you. To make a new file, do File -> User Files -> New User Notes... Once you have your file, simply click in a reference and type Command-U (or Selection -> Edit User Note, or Right-click -> Edit User Note) to add a note to that verse.
Now, if you'd rather organize your thoughts in a more generic, less verse-specific fashion, you probably want that to be part of a User Tool. Create one again with File -> User Files -> New User Tool.... Then, you can edit it in any structure or format that you'd like.
2) I'm not sure what you mean by Workbook, could you elaborate?
3) The Accordance Help that opens in the browser is your full help documentation. As you noted, it is accessible in Help -> Accordance Help. We've had a couple other users report their help opening blank. This is due to some new security settings by Safari in Mountain Lion that seems to affect some users. You have a couple of options:
a: Access the help online, where the same security restrictions don't prevent it: http://accordancefil...V10/Default.htm
b: Use a different browser as your default browser (like Firefox, Chrome, Opera, etc.)
c: Enable the Develop menu in Safari Preferences -> Advanced, then in the Develop menu select 'Disable Local File Restrictions'.
4) Record in what way? You could make user notes for them, highlight them, add their references to a user tool, or my favorite: Add them to a Reference list. To do this, select any references and do Command-Control-R (Selection -> Add Selection to -> New Reference List Tab). You can add however many references here, display them in whatever version/parallel versions, and even save it or describe it at the top.
Let me know if this helps at all, or if you have any further questions!
Edit: Fixed online help URL.