I am also a noob trying to figure out this arduino ide. I have an atmega avrisp mk2 and would rather not use a bootloader to program the chips. avrdude refuses to work for me to program useing the mk2 isp programmer. I get the usb out of sync error. What do I do to setup the avrispmk2 to work as a programmer to work with the avrdude utillity included with the ide software. The hardware works fine to read/write from atmel studio 4 and 6, and I can via atmel studio burn a bootloader to the chip. But I would rather not use a bootloader to burn project, I prefer isp over serial. Thanks for your time reading this mess :).
I split this thread because this seems like a new question.
You can use the "Upload using programmer" menu option.
The USB Jungo drivers that come with Atmel Studio are not compatible with avrdude.
Try this.
Thanks. Got it all working now, appreciate your help..