With regard to Setup A vs B ...
I typically set all of my relievers to Setup A, forgoing a closer and LH/RH specialists. I also use a mop-up. I chart every game and keep track of how many pitches are thrown by every pitcher so I don't go over the allotted maximum until near the very end of the season, if at all. So even if one of the pitchers is still at 100% rest, I try not to throw them more than 2 games in a row, especially if they can be used as a spot starter at the end of the season/playoffs.
So occasionally, I have games where I may only actually have 2 or 3 available relievers. In that situation, I will sometimes set one of the guys I would prefer to not pitch as Setup B, in the hopes that the game will be over before I use the starter and 3 relievers. Most of the time, this works like a charm, and my guy gets a second straight day off. But I have seen on some occasions that the Setup B comes in before the Setup A.
This usually occurs when my team is losing, or in the 8th or 9th inning when my starter has reached his MPC and I am winning by greater than 5 runs. I wish I had boxscores to confirm this, but I don't.
So for the most part, Setup A will come in before Setup B, but I think that Sparky looks at Setup A as a more elite pitcher, and chooses Setup B when the game is not as close and an easier victory is at hand.