Now that we've gotten everything hooked up it is time to program. There are a few different options for programming. Atmel studio is a great option (assuming you are using an ATMEL ARM processor like the SAMD line). Atmel Studio also lets you write programs in C, and compile your code. The Arduino IDE also lets you compile and download a *.hex file of your code. Make sure you download and install Atmel Studio (Windows 7 or later only)
Next, we'll go to the Memories tab, you'll probably want to select "Erase Flash before programming", and then select the location of your bootloader or other code. Hit Program and you should be good to go after a second or 2.