The programming tool in Atmel Studio is the frontend for Atmel STK500. The tool can be used to program devices placed in the target section of STK500, and also external devices. It can also set the various hardware settings as clock frequency, target voltage etc.
For more information, see section .
Since STK500 is a serial port tool you have to tell Atmel Studio that is there. Refer to the section for more information about this.