I noticed there are some creatures with a Fly speed listed in the stat block, and I found this line on the page of how to interpret stat blocks: "Fly means it can move through the air."
Really, I wouldn't worry about this much, it just means they can ignore diffictule terrain features and move over creater's spaces instead of having to go through them. Otherwise I didn't fidn any detailed treatment with a quick look.
In my game I just think of the battlegrid as in 3-d squares. If you type in "flying bases" in the search box here at Paizo, you will find a ton of props you can use to help simulate minis flying.
Also, detailed rules for flying can be found on the PFSRD.
Hope that helps!