Communicating with Arduino Mega 2560 Serial ports through x2 RS232
Your main problem seems to be confused by all the information. I will give you some more.

The Arduino speaks UART (Universal Asynchronous Receiver Transmitter) with it's Serial interfaces (there are 4 of these on the Mega). This is partly the same protocol as RS232, but it uses TTL logic levels (in this case the levels 5V and 0V), while RS232 has different voltage levels and more lines (like control lines). When you connect your Arduino to a PC, the PC is not directly talking to the Arduinos chip (here the Atmega2560). Instead every Arduino with a USB port has an extra chip. It will handle the (very complex) USB communication, so that you can see an emulated COM port on your PC. The data, that the PC sends to that COM port, get's transmitted over USB to that extra chip, which in turn will convert it to UART signals and send them to the Atmega2560.

All Arduinos, that I know of, have only 1 USB-to-UART chip. But you can add your own USB-to-UART chip to one of the other Serial interfaces. You can use a FTDI chip, an Atmega16U2 or (if you don't want to program an extra chip) simply an USB-to-UART converter cable/module, which you can buy and use directly by just connecting their pins to the Arduinos Serial pins.



By the way, it doesn't really matter here, if you use USB3.0 ports, since chips this small cannot work with speeds that high. All these chips use USB2, more is not necessary, they aren't fast enough.