Congrats on the purchase. Its an underrated game. Its right up there on my fun factor list with a couple other pins you have (Met and IM).
To my knowledge, the Iceman ramp should work as follows:
When you start Iceman's mode, it moves from the right to the left and stays there until you hit the first Iceman shot. Then it moves back and forth every few seconds. Hitting Iceman a second time finishes the mode, and you get extra points if you hit it with it over to the left (triggering the left inlane switch).
In Sabertooth, he moves back and forth when you hit Wolverine. Each time you hit Wolvie, he moves to the other side and it changes which side's shots count as hits to Sabertooth.
He also moves in Magneto's mode, but I can't recall for sure when.
Other than that, I think the ramp should stay on the right.
As far as stacking, pick what you like. I have all stacking on and I really like it (its preferred that way by most all of my guests too). I have tried hero/hero stacking off, and I just didn't like it as much. The nice strategy part of all stacking on is you have to get Magneto's SJP AFTER getting all heroes at least flashing (don't need to complete them), and you have to get the Mag SJP in a 4 ball multiball. Hence, you usually have to try to get Phoenix and Rogue shots out of the way early (before locks are lit) so as to not start the Mag MB before getting all heroes. Or else you have to get Mag started again for a second time.