Missile units will fire over a friendly unit in front of them if the missile unit is far enough back and the enemy is far enough away from the front troops to make a safe arc over the heads of the friendlies and down into the enemy. The problem with Naffatuns is that their range is so short that they rarely get a shot off before everyone is all bunched up together. The reason they were going through the motions but not actually throwing their flaming balls of death was because the conditions would become correct for a split second but then the enemy would move slightly and they would no longer have a firing solution.

My Naffa tactic against infantry can take heavy losses but inflicts even greater. Build at least 4 Naffas and put them in front of but as close as possible to your other troops, with Skirmish OFF. When the enemy comes, 1 or 2 enemy units will get a huge barrage right in their face, maybe even twice. If they don't rout right away, at least their charge will be broken as the men recover from the explosions. Charge your main line forward and and retreat your Naffas back, hopefully only a few will get killed. The problem is that some enemy units will be untouched (since you were concentrating your fire) and will make it to the Naffas, but it is more important to get 1 unit to rout, or close to routing, rather than doing a few casualties to every unit.

The "crossfire" tactic excellent as well, a key to using Naffas is to try to get them to deliver enfilade fire (along the long axis of the enemy).