X11 is a windowing system that runs on many platforms. It's like another layer of the operating system. Bibledit was built to run in X11 instead of directly in the operating system so that it would be more platform-independent.
Mac OS X Xcode Tools are a suite of tools for developing software on the Mac. They are needed in order to build Bibledit from the pieces provided in this download.
MacPorts is a tool for downloading and building software packages from the Internet. It is needed for getting other packages that are part of the Bibledit installation. If you have another tool you are comfortable with, such as Fink, you could use that instead. This is done at your own risk and is not supported.
Gtk2 provides graphical functions that Bibledit uses to build its interface.
Sqlite3 provices database functionality, which Bibledit uses internally for storing all kinds of data.
An endnote is a footnote which is intended to be printed at the end of the book, or perhaps even at the end of the entire body of Scripture text being typeset. There could be many notes marked this way. Some translations might choose to set some notes as typcial footnotes, and others as endnotes. Some versions do this in order to distingush between "essential" textual/translation notes (marked as footnotes), and other less critical notes (marked as endnotes).
Looking at e.g. the UK CEV, one might get the impression, that footnotes are explanations of background to a passage and endnotes concern textual variants and choices.
A reference refers to a Bible verse. It consists of a a book abreviation, taken from the Biblical book abbreviations list, and a chapter number, and a verse number. The verse can be a single number, or combined numbers.
Examples:
Genesis 10:5
Matthew 5:6,7
Mark 2:1-3a
USFM means Unified Standard Format Marker. This is a text format common in Bible translation.