Hello ctbenery,
That 4 pin header (DEBUG) is a serial wire debug protocol (SWD) connector. It is another simpler protocol that only needs the data and clock lines to talk via serial between the SAM3X8E and the debugger.
In reference to dealing with surface components on the Due, I would recommend to be very careful. It happened to me twice that a capacitors just pop up the board and where hard to find in my workbench floor :). Regards!