From the demo video's of ISBoxer, you make sets which you choose from when loading.
Basically make a Prot Pally, Elem Shm, Elem Shm, Elem Shm, Disc Priest set.
Then make a Feral Druid, Elem Shm, Bal Druid, Destro Warlock, Disc Priest set.
Then make a etc...

To load it looks like they start ISBoxer first.
Then click launch game from its toolbar, which has an option for each configured set.

Basically when making the set, choose modifier keys for each toon.
It would be easiest if every toon on Account A had the same mod keys etc.