Flying Creatures and AoO

[Provos]

So how is 3d battle handled in pathfinder? How many 5' cubes does a medium/small creature take up and Threaten? I would appreciate any clarification and book/pg references thanks.

[kyrt-ryder]

To the best of my knowledge, 'space' as dictated in the rules is space, whether it's two-dimensional or three-dimensional. It's noted as squares because 3D combat isn't very common, but the same rules apply. Someone with 10 feet of space and 10 feet of reach will threaten enemies between 10 and 20 feet in the air (and fills up space between 0 and 10 feet.) Of course, this comparison sucks when you realize that a lot of the large:tall creatures range from 9ish feet tall to 16 or more, so... use your DM discretion xD, rounding to the nearest 5' cubic increment might work best best.

[Starglim]

A Medium or Small creature occupies a space 5 feet high and can reach 5 feet above or below its space. Don't think about it too hard.

[Quatar]

Rule of thumb: You still only threaten the squares adjacent to you on the 2D battlemap (assuming medium and no reach weapon). If an enemy enters that square and does something to provoke, then you check if he's too high/low to be in actual reach.

I know it's not perfect, but considering it just doesn't happen very often, it's just alot easier to do it like that than to actually try to imagine and somehow use a 3D map all the time.

Edit: Just realised I wasn't actually answering the question. I'd say Medium creatures take up 2 squares above each other (they're usually taller than 5 ft) and threaten one square above that. Small creatures only take up 1 square and also threaten 1 square above that.
But I don't think there's a RAW for that, that's just how I'd do it