I used to use Atmel Studio 5, just downloaded the software and ran it.
Uses the Jungo driver for the MKii, which the IDE does not.
Don't know if 7 is much different.
I was mostly just burning fuses and installing bootloaders, was a lot quicker than the IDE as it did not write the entire memory to do that.
Studio 5 took a long time to start up, haven't tried it or later versions with my new i7 based notebook, the IDE burns fuses & bootloaders quick enough now for the few times I do a set of chips, generally 328Ps and 1284Ps. Will be doing some 2561's in the near future (similar to a 2560, just fewer ports).