Sane,
The questions you ask are common to man. I doubt any Christian who truly has thought through his or her faith, would not either have had the same questions themselves or would not have had them asked of them. So please keep asking.
Now.. I'll break my answers up into three posts, to help with clarity of answers. For me, as well as for you as you read them.
firstly...
1. Why didn't God just poof them out of existance?
Because as I said in my previous post, according to Genesis chapter 12, he was out to BLESS the entire world. According to John 3:16, he was out to save the entire world.
Now.. there are countless times in man's history where the old saying "you reap what you sow" is very true and some of the other forums such as those looking at homosexuality and adultery show that plain common sense says.. "you reap what you sow".
God didn't just destroy them supernaturally for a number of reasons...
1. God never acts in judgement without warning first. You only have to read the account of the flood to see that in Genesis 6 and also in the destruction of Sodom and Gomorrah in Genesis 18 and Genesis 19). You see it to in the way God warns Israel they will go into exile for their disobedience.
Yes, God did use Israel to destoy the Amalekites, but he didn't do it without warning. In this case, the offenders had gone so far into evil in their attitudes, behaviours and lifestyles that God ordered the entire nation destroyed. Very different from Sodom and Gomorrah where God said he would save a few for the sake of their righteousness.
Remember, God only ever works within the bounds of His only Holiness. He cannot work outside those boundaries and remain Holy. Holiness requires Justice.. Justice requires consequences for sin. In this case, sin is not just affecting the Amalekite nation .. it is affecting all those around about it. God's judgement and the way to protect the world, was for every part of the Amalekite nation to be destroyed.. BUT.. look what actually happened.
1Samuel 15:4-34
In response to the command of God
1. Saul warned the Kenites to move away before he destroyed the Amalekites so that none of them would be caught in the middle of the war. because you showed kindness to Israel when she came out of Egypt (unlike the Amalakites who had tried to take advantage of her and kill her.. which in the end was to try and stop the purposes of God to make Israel a nation that belonged to God and would show all other nations the way to God.)
2. Saul did attack the Amalekites but he did not do as God commanded and destroy everything.. instead he took the Amalekite king hostage and he kept the best of the booty for himself.
3. God came to the prophet Samuel and told him he was grieved (upset) by what Saul had done and Samuel went and spoke to Saul
4. Note what Saul had done... "Saul has gone to carmel. there he has set up a monument in his own honour". Saul, instead of giving the honour to God for the victory, which would have been a sign to the surrounding nations that the God of Israel was THE only one true God has instead built a means of honouring himself. He then lies to Samuel (which in effect was lying to God as He knew that Samuel had been sent by God as he knew Samueal was God's prophet)
5. he then tries to justify his actions when he is caught out, by saying that the cattle and sheep were for sacrificing to the "Lord your God". (yet don't forget he had just come from honouring himself on Mount Carmel).
6. Samuel then tells Saul what God thinks of Him. God had take Saul at that time a "no body" and had then made him king over Israel. To understand the significance of this, you need to know, that until Saul had been made king, Israel knew only one king.. God himself. They had pled with God to let them be as other nations around about them and to have a king of their own. This king, within a short time of his crowning, had started to lead them away from God and worship and into the practises of the nations around them (like the amalekites).
7. God tells Saul the reality.. the truth for any one on this planet.. obedience is much more important to God than is sacrifice.
You see.. what was at stake here, was God's glory, Israel's commitment to the covenant promise that they would be a nation to bring blessing to the rest of the world and also the sins of the Amalakites was ever before him in the way that Samuel spoke as he killed the Amalakite king
"As your sword has made women childless, so now your mother, be childless amongst women."
So.. that is the answer to your first question ) see how I go with the rest.