The project properties has an optional override of the serial port used for debug. LocalPort/RemotePort. For example LocalPort=COM10 and RemotePort=Serial2. Leave empty for the default which uses the standard Arduino usb/serial connection used for upload.
The local port relates to the pc and the remote port relates to the port the arduino will use for serial debug. Please note that some arduino boards have a single hardware Serial port, such as the Arduino Uno. Others such as the Leonardo have Serial, Serial1 and some such as the mega2560 have Serial,Serial1-4. For advanced users, LocalPort can also contain the name of a valid pre instantiated (prior to setup()) "compatible" object.
It is also possible to override the port speeds (LocalSpeed/RemoteSpeed). Normally the Remote and Local speeds will be the same unless remote devices such as xbee modules are being used.
If hardware serial port(s) are unavailble or if you prefer to debug using software serial then select “SoftwareSerial” from the RemoteTransport property.
Software serial defaults rx/tx to pins 7 and 8 but you can use the RemoteRX and RemoteTX project property to change to something else. (tip: In this case leave RemotePort empty)
It is recommended that speeds of 57k (recommended) or 19k are specified when using SoftwareSerial (especially if altering variables on a running microprocessor)
When using SoftwareSerial, leave the RemotePort property empty unless you already have a custom SoftwareSerial object in your code that you want the debugger to use (not recommended or tested).
You do not need to add the Arduino SoftwareSerial library to your project to debug using SoftwareSerial.
If you change the local port to a fixed value then that port will always be opened as a debugger after clicking F5 (or menu "Debug>Start Debugging").
If you want to use, for example, Serial2 for debug instead of the main serial port for debug then enter "Serial2" (without quotes) into the "Remote Port" property.
As stated earlier, SoftwareSerial allows you to define the pins to use for TX and RX. FastSerial works the same as HardwareSerial. To use FastSerial you must already have a project that initialises it then you can use the "Remote Port" property to define the name of the serial object. If "Remote Port" is empty then the "Serial" object is used by default
note: any property can be empty for defaults to apply
apm: If you are using the hardware serial ports of arducopter or arduplane then use the“FastSerial” option.
How to connect arduino pins to the computer using rx and tx pins (or serial1,serial2, etc)
There are lots of different cables and usb/serial converts.
FTDI 5v Cable (there is also a 3v version)
(you might find it cheaper or a better alternative elsewhere)
Use the schematic to detrmine which two pins (rx and tx) to connect.
Rember to cross the rx/tx between pc and Arduino (rx>tx and tx>rx)