Thanks for the resources brother. I was once talking to an atheist friend and I told him absolute moral right and wrong exist because of God's law and he responded saying that in wars and similar situations people(Christians) justified killing others though in other cases murder isn't justified by the same standards, yada yada ... making the point that morality is governed by society.
I didn't really know how to carry the conversation further.
First off I completely agree with my two brothers who commented. The trick with presuppositionalist arguments is showing in love how they assume that which if they were consistent they would have to deny.
Now in that situation I would remark that war is inevitable in our world. So whether God exists or not (Van Til called this stepping into the ground of the unbeliever) war would still be here, so their atheism doesn't solve that.
Then I would attempt to take them through just war, war crimes and anything else natural law teaches us about how to handle violence.
Then I would say I have a better answer and hope than you I think. I believe natural law is key here.
You see Van Til taught us to take advantage of the image of God within, moral law and all, and general revelation outside. They know they are God's creatures and owe him obedience and worship.
You see a sociological basis for morality is a logical fallacy. I would then try walk them through the great history of redemption. That God Himself had to come down and solve the problem for us, in the son incarnate.
Then say on your basis for morality is just a logical fallacy but on my basis it is part of a grand history of saving us from the worst problem we got ourselves into.
They know they are accountable to him, why else would they try to blame him for our problem. Don't point that out to them but just remember that's what's going on. That's taking advantage of what we know they know deep down inside.
Then I would agree with them about how horrible war is and that you understand why they feel that way. But in your worldview (Van Til called this asking them step onto your ground) you can have hope because he solved it for us and they can keep their logical fallacies but you'll keep your history of hope and reason. Then see how it goes.
Disclaimer this is a large template for a method of handling this question. Obviously I can't anticipate all the different ways a conversation can go. So in love and wisdom take the big picture template I layed out and adjust it to your needs.