To start things at a basic level, I would suggest adding the Reference prototype to your document from File > Built In Prototypes > Reference. Use Reference as the prototype for your notes about source documents. You might want to create your own Concept prototype and use that for the notes about terms.
To link terms to sources, or terms to terms there are many options – 1) create links between notes on a map or in the outline, 2) use links in the body of the text of a note, or 3) use footnotes.
- There are lots of ways to create links on maps or outlines. Read all about the concepts in aTbRef For example on an outline
- Links in the body of a note can be made like this (a bit clumsy in the video, but what’s happening is I am using Tinderbox’s facility to suggest link completions):
- Footnotes. Select some text in a note and choose Note > Footnote > Add Footnote As Sibling /or/ Endnote
Other contributors can suggest more and better options for what you want to achieve – use of the link parking space, use of smart adornments, use of attributes such as $Tags, and so on. I strongly suggest reading The Tinderbox Way v3, by Mark Bernstein the author of that and of Tinderbox.