In order for your PC to "see" your Arduino, your Arduino board most probably has whats called a USB to serial converter chip. When you program your Arduino from the Arduino IDE, what actually happens is that the pc speaks with the USB to serial converter,which in turn talks via serial communication with the microcontroller (that's the ATmega). That is, unless you are using Arduino Leonardo or something else with the ATmega32U which also has built in USB. But basically, you make a serial connection from the PC to the device via USB.
LPC1343 and its bigger brother LPC1347 have a different strategy entirely. These chips have a bootloader in ROM that is capable of identifying itself as an USB mass storage device. What this means is that when you plug in your device the bootloader can make the device pop up as a removable drive on your PC. Programming the device is simply a matter of deleting the firmware.bin on the removable drive and copy pasting your own firmware (a .bin file) into the now empty drive.
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Do not be alarmed by CRP_DISABLED - it simply means that "Code Read Protection" is turned off in the device. This is normal.
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