Notes vs. Highlights vs. Clippings?

I'm going to answer your second question first since it may clear up some confusion in the first question:

- How do you access a highlight note from the highlight itself without basically turning it into a note?

You don't turn highlights into notes. Highlights and notes are functionally the same in terms of what the program does. So think of it as "notes-and-highlights" instead of "notes OR highlights." Whenever you create a highlight you are actually creating a highlight-note. Whenever you create a note you are actually creating a note-highlight. For most purposes, the only difference is the point of interaction (explained below).

Given that, I'm not sure I understand your question about access or whether it's still relevant. You can open the highlight-note by right-clicking the source text where the highlight is displayed and select "Open notes and highlights" from the dropdown menu. Or you can access it by opening the notebook. 

- When do you make a note vs a highlight?

1. If you start by creating a highlight, then the point of interaction is in the display of the highlight you've created on the text. If that's all you wanted to do (like merely highlighting in a book) then that's also where your interaction will end. You don't ever need to do anything with the fact that the highlight is also a note (though this can be used in the future for filtering/searching, I think). But if you want to add text ("a note") to that highlight (maybe immediately or in the future) then you can find and open that highlight-note (right-click method I mentioned is one way of doing this) and add text to the highlight-note.

If you add text to a highlight-note in this manner, you will likely also want to also add a note-icon to the highlight so that the source text, which you've highlighted, will signify that there is text written on the highlight-note. (Otherwise you may forget and overlook the fact that you've added text (or "a note") to the highlight in the future.)

In the notes file itself, this is where you set an icon to be displayed in the source-text:

2. If you start by creating a note, then your starting point of interaction will be in a note-and-highlight file where you add text. The source-text to which the note-and-highlight is attached will automatically display whatever note-icon and highlight you last used. 

So whether you create a note "or" create a highlight will depend on whether you primarily want to write something down or primarily want to create a visual call-out. But ultimately the two operations are the same.

- Are clippings more of an intermediary step/holding tank for info or are large quantities of clippings a viable way to organize information?

I can't help you here. I don't understand the value of clippings given the way notes now function, aside from organizational preference. I think in the older versions of the program, where the note system was not as robust, clippings were useful for certain things. I don't see the value of them now and maybe they are just a carry over for users in the past who created a lot of clippings. People sometimes keep "personal books" in the sense of a collection of quotes or notes they've made on 3x5 cards throughout the course of their reading and research. Clippings were useful in that regard and might still be useful if one likes the way clippings organize and display information on a topic that feels like the digital version of a personal book. But, as far as I know, they don't fill in any holes or gaps in terms of what you can do through notes-and-highlights... maybe other users know more about this. 

The way I use clippings are for the short term. I use clippings in sermon prep for the upcoming sermon and then delete the clipping document once done.  It allows me to have all my commentary research in one document instead of multiple notes.  I use notes and highlights for things I know I''m going to come back to.