Most alternate munitions have to go to the specific munitions to understand the specifics, but there are two general types of attacks you can make with them.
standard weapon attack: Uses the base damage values (the main ones on the unit card), but the alternate munition modifies the attack somehow.
special weapon attack: Uses the special ability damage values (the ones listed with the special ability, like LRM1/1/1).
A Swarm LRM attack uses a standard weapon attack for the initial attack, but if it misses it can make a special weapon attack against a nearby target.
A Flak AC attack uses a standard weapon attack, but if it misses an airborne target by a small margin of error, it can deal the special weapon attack damage.
Precision AC ammo requires the player to make a choice before attacking. Make a standard weapon attack and add more damage, or make a special weapon attack (using only the AC damage) but get a better chance to hit with the attack.
So while the concepts of standard weapon attack and special weapon attack are generalized, how they are used depends on each specific alternate munition.
For dead-fire missiles, you would make the same adjustments you would make for a special weapon attack to the standard weapon attack. In your example of a 5/5/5 base damage value with LRM3/3/3, using dead-fire missiles, the LRM would adjust to 4/4/0. The standard weapon attack, using dead-fire missiles, would become 6/6/2. You add 1 at short and medium range, but lose the LRM's long range damage (hint, you wouldn't use the dead-fire missiles at long range anyway).
