The usb port is used for programming the arduino. Once the arduino has been programmed the serial port is released for other serial communication.
The arduino IDE has a serial monitor which can be used for sending and recieving data. However, that is all it does! If you want something to happen on your computer when you press a button, you will need to use another programming language. If your new to programming then Processing would probably be a good start as the arduino language evolved from that!
The only thing you need to worry about is that you close the serial port in the programm on your p.c before you attempt to programm the arduino!