I tend to use them all as one unit. I select them and try to have equal numbers of them for a balance of offensive and defensive power.
When nothing is happening, set waypoints for them to patrol to look out for attacking forces (particularly useful in the skirmishes).
They're especially useful as spotters since they can see beyond the ground forces' view. Set them circling out of range of enemy fire and they can see targets for your mobile artillery, even if it's not a constant view.