After some "getting the band together" with a new FC group got into a modified beginning of Cleansing of Black Spur last night and was blindsided by an Elf PC with his Giant Eagle.
I was ready for Wyvern vs ground-based party, the addition of an extra flying combatant put me into Ad Hoc mode because I couldn't remember if FC handled flying combat, the players were all fine with a simple solution and me checking later. Checking back, as it appears the core doesn't closely discuss it, here's the solution I used, with some minor tweaks made in the light of day and a search of the forums -- comments and suggestions appreciated.
---Ad Hoc Solution---
After checking the Fly spell, here's what I went with
Effect: The target may ascend at 1/2 this Speed and descend at twice this Speed. Because the target isn’t anchored while flying, his Size is considered 2 categories smaller when resisting Bull Rush and Grapple actions.
Ad Hoc Ruling:
Characters that fly by wings (versus say Beholder-style perfect levitation) function the same way:
A) Must move a minimum of 1/2 their Fly Speed to stay airborne
B) May ascend up to 1/2 their Speed and descend at twice their Speed in feet as part of their move (i.e. choose to climb, dive, or fly level)
C) Any flying figure has a d10 next to them to count altitude in 10' increments
Beyond that, I ran it essentially the same way Krensky mentioned here (great minds and all that

)
As for aerial combat, flyers move up to their flight speed. If there's a question about whether they can do something or fly in tight quarters, make an acrobatics check using the Maneuvering Room section of table 2.17. GM needs to determine DC on the fly, so typically you should use the sliding DC table (7.22) on page 370.
This works pretty well and I'll keep using it when doing Air/Ground combat. But in the cold light of day I want something that feels a little more simultaneous and doesn't put me at risk of having to run through the Pythagorean theorem in my head during a game
What I want is essentially a Joust mechanic, so here's my first thought -- anyone want to take a swing at it?
Counter Charge (Charge Trick): The character reacts to an incoming Charge from a flying opponent. Once per round when not adjacent to an opponent, you may make a Will save (DC equal to the 5 + 2X the difference between the Current Initiative Count and the Initiative Count you would usually act on.
With success, you may simultaneously counter-charge the charging opponent. Any free attacks made as part of a Run (or should it refer specifically to the Charge trick?) using this ability are made against an opposed Maneuver check rather than the target's normal Defense. You may use this ability a number of times per combat equal to your starting action dice.
Help?