You are correct on how the Rank minuses work. And someone can correct me if I am wrong, but for maintaining the power you would stack the minuses from the rank differential and the maintaing penalty together.
I think with a 3D6 bolt all the damage hits one target. So, if I am facing off against a Wild Card I want to make sure I put as much damage at that target so if he chooses to soak he has to take the lump sum. If I fire off two separate bolts that will be two separate soaks and more likely each hit will be less damage thus easier to soak. For me I would want to use the 3D6 against a big bad guy and in the case of fighting mooks, split the bolts and hit two targets who will go down with one wound. Just keep in mind that the two 2d6 bolts don't stack up into a large numbered damage, but two separate attacks.
And you can decide before you cast which bolt combo you use.
That's what I thought with the minuses, and it makes sense... it's just that I've been unable to find a page reference to point to my players in either the AoO hard back / pdf or in the Savage Worlds Deluxe rulebook.