There is jus ad bellum ... the determination of whether or not going to war in a specific instance is just (i.e. Just Cause vs. just because);
and then there is jus in bello ... the determination of whether of not a war was fought justly (i.e. means of war, rules of engagement).
Just War theory is bellum iustum, and is simply a discussion of whether "war" as a concept is "right" or "good". And if so, how does one limit war, if one should.
The goal of war is never annihilation, its neutralization of a threat to one's ability to obtain an objective. War is a means to an end, not an end in itself, therefore the end determines the rightness of the war, and the limits of the war. On its smallest scale, consider your baby child. It wants to crawl over to the outlet and put its finger in there ... but that violates your objective to raise a healthy child. So you begin by saying no; doesn't work. You escalate force, and say no and pick the baby up and carry it across the room. It promptly crab walks over the same socket, hell bent on poking its digit into the socket. This time you say no, and smack its little claw. It cries, gets mad, and reaches for that socket again .... so you snatch up your axe, and lop its hand off. That'll teach 'em, they can't stick their finger in the hole!
Probably not ... you have a reason bigger than the violence that limits the violence itself. In a defensive war, the lines get blurred, the individual feels personally threatened, the baby is going to stick your finger in the light socket. The desire is to stop the agression, and it becomes a battle of wills. This is where many feel like there are no rules, my life is at stake - I must defend it any cost.
But at what cost to the soul? For many the thought of violating a moral code, even when faced with death, is horrific - death before dishonor. This then limits what a man will do even when threatened with death. Jus In Bello is that conversation in the defense - how far am I willing to go before I cross the line of good, just to protect my own worthless neck.