As velocity101 said, it will not provide power. From reading the user guide
The Atmel AVRISP mkII supports target voltages from 1.8V up to 5.5V.
VCC must be connected to the target board in order to get correct operation and voltages on the ISP/PDI lines. VCC does not draw any power from the target.
In fact, the AVRISP mkII will not detect the target until it (the target) is powered. Also (I can't find the quote right now), I read somewhere in the user manual that the programmer senses the target voltage and adjusts its self by level shifting to the correct voltage. I do know when you enter the programming dialog it displays the current target voltage.
Hope this info helps.
BTW I was here a few days ago and found a thread on how to get the Arduino core to work under Atmel Studio 6. I followed the instructions and it worked! For me anyway. But after messing around a bit, I'm having some minor troubles. So, I need to find that thread (that's what I was doing when I came upon this thread) and follow the steps again. It's really cool
having all those libraries playing nicely with a full featured IDE with debugging capabilities.
So, I'm off to search...