That segment of stay puft is timed, so you don't want to get too greedy or you will lose your multipliers and have to requalify the mode. (been there, done that) Think the timer is 35-40 seconds and I don't think it pauses if you cradle. If you have the 2x or 3x target lit during this time, try not to hit either until you've locked in your mode multiplier.
Once you hit one of the major shots, that multiplier applies to all the lit mode shots, not just that shot. In case that wasn't clear. So aim for whichever multiplier is the biggest, not your favorite shot.