Mods, effect "dice," and order of operations

I was listening to SCRPG Live season 2, and Christopher used the rules differently from what I've been seeing.  He declared he was using a bonus before he rolled, but then after he rolled he decided what die the bonus was going to apply to (since it was an ability that keyed off both the mid and the min).  There are mentions in the rules about who gets to decide which die a mod applies to, but not when they make that decision.

... all of which reminds me of another question I had and which hasn't been officially answered, to my knowledge.  It's possible for multiple effects to trigger off the same die (notably twists and some Red abilities).  The rules suggest that mods apply to an effect die, and not the effect itself.  So, for instance, say you use an ability that keys off Mid, and add Inspiring Totem (make an extra basic action) to make an Overcome, which triggers a twist.  The GM picks a twist that also keys off the mid die.  If you had a +2 to that roll, does it apply to the Inspiring Totem Overcome?  Does it apply to the twist?

I've only listened to the 1st 5 episodes of Season 1...all this week.

My understanding is that a bonus must be declared before the roll, and generally the bonus is going to be applied to the result (because only one die applies).

If 2 dice are used for the result, it then seemed that the results are determined first (max-mid-min) and then the bonus is applied to one of them.

If I'm right in my memory, that should be more clearly specified in the rules.  I don't think it would make a difference very often, but I think it matters if ties are rolled.