AVRISP MKII does not appear in AVRStudio 4 (latest build 4.18 SP1)
Programmer selection in AVRStudio is user experience nightmare.

Are you going to Tools -> Program AVR -> Connect ?
And in the "Platform" list you should see "AVRISP mkII" as one of the options with "USB" as the only available port.  

This should appear whether or not you have the programmer plugged in.  If you're missing it, it sounds like you may have an incomplete install of AVRStudio.  (I don't recall, but I think AVRStudio might install a USB driver or two during its install)