USB is supported.
On the second tool bar (the lower one), to the right of the text window, there are three black clickable items, click on the one marked 'con' and you should get a window which will enable you to choose your programmer. Choose the avr isp mkII and then you will get a window with menu tabs marked 'program', 'fuses', 'lockbits', 'lockbits', 'board' & 'auto'
The 'program' tab will let you select your device, and the 'board' tab will let you select your speed. Remember to click on 'write' after selecting your speed. Then go back to the 'board' tab, in the box marked 'flash', to select the file you wish to upload and click on program to upload it.