Part of the reason you can't find anything is because the serial ports can be setup in so many different ways that it depends on you to figure out how you want it.
additionally there are changes to the firmware to allow even more serial ports then the default you see on the configuration menu, but these require changes to the source code to the Arduino firmware on the DUE.
there is also limitations on what software you may use for your O/S.
most people will use CP/M 2.2 or CP/M 3 there are special versions that allow you to change the IOBYTE which is serial port mapping within the O/S but it is limited with off the shelf software.
back in the day most users had 2 serial ports, 1 would feed the terminal and the second was used for a printer or a modem or a null modem connection to another machine or device.
you are also limited with baud rates due to a bunch of factors 9600 baud is your basic go to as it usually works fine.
-----
The way i use my serial connections.
the micro USB on the back of the Altair-Duino pro works a little different then a standard RS232, I have it mapped to 2sio2 port 1. In order to use the 2sio2 serial ports you need to modify your firmware and enable it.
Without patching the firmware and reuploading to the DUE you can map the microUSB to 2sio port 1 or 2 however 2sio port 1 and SIO is needed for the disk and terminal interface so your left with just 2sio port2 for mapping which would overlap with the other possible serial configurations.
the 9 pin serial RS232 could also be mapped to the same 2sio port 2 or as SIO primary for the terminal. if you have a pro with a GEOFF Terminal that it would already live at SIO primary.
what i like to use my micro USB for is a usb connection to a modern computer i use Terminal software teraterm or putty to transfer files back and forth i modified PCPUT and PCGET to use the higher Serial port of 2sio2 port 1 or 2 over the standard 2sio port 1 or 2. I treat it like a network disk share in this way. just transfer files i need between both computers without disturbing my other connected serial devices.
when using the micro USB on the back you will want to install a USB power blocker. The Arduino DUE will automatically switch to power it sees on the micro USB port and that will bypass your front panel power switch and the wall wart supply and cause problems when you need to cold boot the machine. If you have a large power load on the Aurdino Due with accessories that can overload the DUE USB port using it for main power and could damage it, so i recommend installing a USB power blocker.
Since i have patched the DUE firmware i have access to 4 serial ports instead of the default 2.
I mapped the 9 pin serial rear port to the standard 2sio port 2 this was the default under CP/M for using a modem or a serial printer port. (pin A6/A7) LST: was used for printers and modems (you can think if it like a com port on a PC)
most serial devices connected to this port will require a null modem adapter to swap the TX and RX lines.
for my setup i have a Serial multiplexer Switch connected to the 9pin rear port that allows me to switch between multiple serial devices on that main port without changing around cables.
I have a serial printer, a serial modem, a raspberry pi, and a connection back to my PC with a RS232 to USB adapter.
the connection back to the pc allows me to use CP/M to dump information like it would be to a remote terminal or a line printer using control-P under Cp/M
its a good way to dump fast information i need to the PC via teraterm or putty and again as a fast external terminal. in a pinch i can also change the IOBYTE and remap my primary terminal to the LST: port and switch back and forth from my primary serial terminal to teraterm on my pc allowing for TEK programs to run. extremely flexible.
the CP/M i use is modified to allow the IOBYTE to be modified(in addition to other modifications). Cp/M has a limited number of main serial ports which can be mapped this is part of the reason i have the micro usb mapped on 2SIO2 port 1 so it lives by itself and software is used to access it on its own.
Additionally i have a TX/RX hack RS232 port that allowed me to install a second 9pin rs232 port on the back of my case. this port is mapped to SERIAL (RXL/TXL) and drives an external FABGL ANSI Serial Terminal that is extremely powerful as comparted to the GEOFF Terminal that comes with PRO kits. The TX/RX serial port must also be enabled with a change to the firmware.
I also have a second micro USB port on the back of my machine that is connected to the DUE on the Native Port (default uses the Programming port for the rear microUSB)
that port is mapped to a hardware Dazzler graphics card emulator and allows Dazzler graphics programs to run on my setup.
to keep things Simple if your using the 9pin serial port on the rear, you will need a null modem adapter then connect it to a serial device. this 9pin port uses 3.3-5v logic and many older serial devices may require 12V power in that case you will need a external serial powered adapter like B&B used to make. i have one of those powered adapters that i use as a serial to parallel converter and it uses external 12V power to feed the connection.
you may need to juggle quite a few different serial port connectors and adapters to get something working but it does work.
there is so much flexibility in the setup you could almost do anything as well.
the easy first step is printer or modem connected to the port. that will give you the ability to output information on paper. a modem will allow you a bunch of options as a modern wifi modem can create a virtual serial bridge between two remote machines. in my case i use the wifi modem to create a virtual serial bridge to a remote Altair computer and i can transfer information between both machines i can even remap a remote terminal and drive one of the altairs remotely as it thinks i'm in front of the machine with a directly connected terminal. wifi modems are a little limited and temperamental so i have a raspberry pi connected to the serial switch as well allowing, telnet, ftp, and WWW browser access to the internet. wifi modems are limited to telnetBBS or other remote machines but there is a bottleneck and they are much slower then your connected baud rates. for fast transfers i just link 2 raspberry PIs together and transfer over FTP.
i can keep going but you should get an idea of what is possible which is quite a lot.