The more thoroughly you mix the better and most manufacturer instruction tells you to scrape the sides of the container as well.

When I am going to glass a boat, I start saving tomato sauce jars and use them and shake up the epoxy. I pre measure out some two to one mixtures and put black lines on the jars with a sharpie and do a good 1/3 of the jar size batches. It's really fast and I have never had a problem with the supposed air problem. I pour it on the glass and squeegee it out. I always pre warm up my epoxy first as well to thin it out. After a few batches, I change over to a fresh jar so any epoxy that is starting to thicken is not in the mix.