1) While this is probably difficult for MASS combat, I've often seen people use dice under minatures to represent 5' elevation levels. Different colors/transparencies can mean different levels (i.e. an opaque die represents 25' but a translucent die represents 5').
2) Ignore diagonal movement in the 3rd dimension and just count all elevation changes as 5'. It gets too messy to calculate "Ok, what if I move diagonally and 5' up to the square to the upper NE, how many squares does that count? Do I have a half square of movement carrying over from my previous move? Arrrrgh! I forget!" It's fine to fudge that IMO as charging a full 1 move reflects the difficulty of gaining altitude/energy.
3) While this is obvious in some ways, make sure you understand the flight maneouverability rules well. Lots of players forget minimum movements, to reduce 5' from movement for a turn at low maneouverabilities, and the like.