Right, you need the keyboard handler script. In fact, the keyboard handler script is where any customization for a particular vehicle type is done. And yes, you are missing several parameters there. If you are using 2.2beta3 the missile counters are arrays, and the names parameter is also an array of names:
[["bh1"], 0, "", [0,0], [0,0], 10, 10, "mando_missiles\units\mando_missilevehicle2.sqf", false, false, false, false, [4,0,-2], "mando_missiles\units\keysets\mando_air1_keys2.sqf", 5, 5, 2, 0]execVm"mando_missiles\units\mando_assignvehicle_by_name.sqf"
If you want a direct implementation of flares in choppers, check mando_remote mission, there you will find two Cobras with missiles and flares, just use the same script line setting the missile counters to 0.
In the example above, 10,10 means [maximum flares capacity, initial number of flares] and then the targeting hud is set to 5 horizonta degrees and 5 vertical degrees. Note that this is for targeting, not for incoming missiles, incoming missiles are marked always no matter its angle relative to the chopper heading.