This page shows a couple of techniques - Notes, and including pre-prepared trees (output from a perl program run locally).
Including Notes using REF
This shows and easy way of inserting notes which are collected and displayed as footnotes. The notes are hyperlinked (both ways), and so if there's a lot of intervening text you can switch back and forth between the referring text and the footnote. The note numbers are generated automatically, and the whole list of notes is placed using the REFERENCES plugin.
This is the second note. You can include formatting within the footnotes.