Another approach is similar to the Comments idea, but uses the binder as the place where you write notes. This is better for longer form note taking, or where multiple bits of text are best served by one central set of notes, as comments can only refer to one spot with their highlight.
The basic idea is to select the text you want to annotate, and use the Ctrl+L or ⌘L shortcut to create a new binder item linked to this text. You will be given a dialogue to choose the name and location, and then by default this new item will load in a window where you can work on the text.
To link it to other segments of text, select that text, and then type in a bit of the note item’s name in the main toolbar “Quick Search” tool. When it pops up in the list, drag and drop the item onto the selected to text to link to it. If you’re doing a lot of this, it can be convenient to split the editor and load your notes into one split, then browse and edit with the other split. You can drag and drop the icon from the editor header bar at any time to create a link to it in the text.
As you do this, you will note that the item you are typing notes into will populate its Document Bookmarks list (in the Inspector) with back-links to the sections of your text that referred to it. If you want to get more detailed than that, you can put little markers in inline annotations around the link points. For example each of my larger notes has an identifier I use, and can type this to refer to it from elsewhere. I use this identifier all over the place, even outside of Scrivener, binding ideas with notes, and todo list items and calendar entries and so on.
The technique of identifying two precise spots of text together, in general, is covered in greater detail in this forum thread. I would encourage any further discussion on point-to-point linking to be taken over there.