When running SLI, does it make much difference in temperature and noise between a setup where the bottom card is a blower fan design, and the top is a 'better' aftermarket cooler, VS two cards with aftermarket coolers that dump all the heat in the case.

Well reference cards typically are a bit louder in practice so yes it will be quite a bit louder then if you were to use 2 aftermarket GPU's.

Typically when you use a reference card it does a better job of pushing air out of the case then a aftermarket fan however when you have 2 cards sandwiched next to each other you end up with a lot of heat building up with the cards. And because of this the fans will ramp up and if your case isn't good about dampening noise you will definitely hear it.

So my opinion is that yes it may be more beneficial to get a aftermarket cooler card solution then a normal reference blower design solution if acoustics matter to you.
So it is better two SLI two aftermarket coolers, rather than have just the top an aftermarket one, and the bottom a blower? Just wondering because I read about people using SLI Gigabyte 670's and the top card getting dreadful temperatures.
Well I would evaluate your case and its design. Questions to ask yourself. I would say that if a card was going to have a decent time with SLi it would be that card because of its slim form factor and the fact it has 3 fans cooling it however it is a longer card its a 680 PCB and it is a 670 that does use a 6+2 power connection in conjunction with a 6 pin so power to those cards will be higher. What about the power edition cards from MSI or the directCUII cards from ASUS.
I would just go in expecting in a multi gpu configuration that if you didn't have good case cooling you would run into issues heat related. I'm not so sure a blower card will really help with that.

1. Does my case have good air flow.
a. Do I have 1 maybe 2 fans pushing air in and 2 pushing air out.
b. Do I feel warm air coming out of my case.
Very much so! With a single card it typically doesn't matter because there is plenty of spacing for the card to breath but in most situations you have 2 cards very close together. Some motherboards allow you to have more then a slot spacing for 2 cards which helps but those are typically more of the higher end motherboards. But yes overall airflow plays a much bigger role :)