I tried uploading stuff to a mega2560 with AVR studio. It told me to upgrade the firmware on the MKII, so I did. Unfortunately, since it upgraded the MKII, I cannot upload the boot loader via the IDE. I had a 2nd MKII, so I was able to upload via the Arduino IDE just fine. So, I guess this means that you cannot really use AVR studio with Arduino stuff? Also, how do I downgrade so my first MKII can use it with my arduino boards again?
Also, if I cannot fix the MKII, how would I go about uploading the arduino boot loader with just AVR studio? Can they really not play together?
You likely are just getting Jungo drivers for the MKii when you need libusb instead.
Search for Jungo in the forum from posts last summer, there is a post that explains how to set up the IDE drivers (which is in the IDE foldes already).
I think hiduino has also posted about a tool that lets both be used, I have not been able to make it work, think my older Vista setup is a little too messed up from years of activity, not everything works right anymore.
I can make it work with both, but not at the same time. Have to switch drivers. I wasn't aware of a tool that avoids this, but that could certainly be very handy.