I got a great answer to this but have more questions. :) I was told that having javascript declared in two different places was bad and messy(you can see in the answer below), but I'm learning from a book right now and it told me to put my variables, arrays, functions etc. in the head of the html and the rest in the body.(that's why I have javascript declared in two different places) Is that wrong and why? He also recommended using a developer tool. I'm very new to coding in general and don't know much about these could anyone recommend a developer tool for chrome? Also what would a developer tool do? Thanks!
This was fixed:
Hi I was converting the card war game so it worked on a page instead of in the console and here was my original code http://pastebin.com/AgLgy97F.  I was trying to use document.write to write out the code on a web, but I found out that document.write rewrote the whole page and removed the button I put there to progress to the next turn. 
I looked on the forums and I looked online and came to the conclusion that I shoud replace it using this<div id="play"></div> and  document.getElementById("play").innerHTML="I'm a string!".  So I made this http://pastebin.com/29mVqp67.  I tried it out and nothing happened -_-.  What did I do wrong replacing document.write?
The new code I made is here too:
<html>
    <head>  
        <script language="JavaScript">
        <!--
var disp = function() {
    document.getElementByID("play").innerHTML="You drew a "+user_disp+".";
    document.getElementByID("play").innerHTML="Your opponent drew a "+cpu_disp+".";
    document.getElementByID("play").innerHTML=statement;
};
var war = function() {
    document.getElementByID("play").innerHTML="W-A-R spells WAR!";
    disp();
};
var full = [1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,6,6,6,6,7,7,7,7,8,8,8,8,9,9,9,9,10,10,10,10,11,11,11,11,12,12,12,12,13,13,13,13];
var user = [];
var cpu = [];
var rand = 0;
//Shuffles and deals the deck
var shuffled = [];
for (var i=0;i<52;i++) {
    rand=Math.floor(Math.random()*full.length);
    shuffled.push(full[rand]);
    full.splice(rand,1);    
}
for (var j=0;j<52;j++) {
    if (j%2===0) {
        user[user.length]=shuffled.pop();
    } else {
        cpu[cpu.length]=shuffled.pop();
    }
}
//Creates a bunch of variables and functions that will be needed in the game
var cpu_card=0;
var cpu_warcard=0;
var cpu_war1=0;
var cpu_war2=0;
var cpu_war3=0;
var cpu_disp=0;
var user_card=0;
var user_warcard=0;
var user_war1=0;
var user_war2=0;
var user_war3=0;
var user_disp=0;
var statement=0;
var card_name = function(cpuc,userc) {
     switch (cpuc) {
        case 13:
            cpu_disp="K";
            break;
        case 12:
            cpu_disp="Q";
            break;
        case 11:
            cpu_disp="J";
            break;
        case 1:
            cpu_disp="A";
            break;
        default:
            cpu_disp=cpuc;
            break;
    }
    switch (userc) {
        case 13:
            user_disp="K";
            break;
        case 12:
            user_disp="Q";
            break;
        case 11:
            user_disp="J";
            break;
        case 1:
            user_disp="A";
            break;
        default:
            user_disp=userc;
            break;
    }
};
//Lets play the game!
        //-->
        </script>
    </head>
    <body>
        <form>
            <input type="Button" value="Click to Take Your Turn" onClick="playWar()"></input>
        </form>
        <p>
        <h1>This Is War Lets Play!!!!</h1>
        <br>
        <div id="play"></div>
        <script language="JavaScript">
        <!--
function playWar(){
if(user.length<52 && user.length>1) {
    //Picks out the cards that are used
    cpu_card=cpu.shift();
    user_card=user.shift();
    card_name(cpu_card,user_card);
    //Figures out if you win, lose, or go to war
    if (user_card<cpu_card) {
        statement="You lost!";
        cpu[cpu.length]=cpu_card;
        cpu[cpu.length]=user_card;
    } else {
        if (user_card>cpu_card) {
            statement="You won!";
            user[user.length]=user_card;
            user[user.length]=cpu_card;
        } else {
            if(cpu.length<3 || user.length<3){
                user[user.length]=user_card;
                cpu[cpu.length]=cpu_card;
            }
            else{
                statement="You tied! TO WAR!";
            }
        }
    }
    disp();
    //This is what happens when you go to war
    if (statement==="You tied! TO WAR!") {
        cpu_war1=cpu.shift();
        cpu_war2=cpu.shift();
        cpu_war3=cpu.shift();
        cpu_warcard=cpu.shift();
        user_war1=user.shift();
        user_war2=user.shift();
        user_war3=user.shift();
        user_warcard=user.shift();
        card_name(cpu_warcard,user_warcard);
        if (user_warcard<cpu_warcard) {
            statement="You lost the war to your opponent!";
            cpu[cpu.length]=cpu_war1;
            cpu[cpu.length]=cpu_war2;
            cpu[cpu.length]=cpu_war3;
            cpu[cpu.length]=cpu_warcard;
            cpu[cpu.length]=cpu_card;
            cpu[cpu.length]=user_war1;
            cpu[cpu.length]=user_war2;
            cpu[cpu.length]=user_war3;
            cpu[cpu.length]=user_warcard;
            cpu[cpu.length]=cpu_card;
        }   else {
            if(user_warcard>cpu_warcard) {
                statement="You crushed your opponent in war!";
                user[user.length]=user_war1;
                user[user.length]=user_war2;
                user[user.length]=user_war3;
                user[user.length]=user_warcard;
                user[user.length]=user_card;
                user[user.length]=cpu_war1;
                user[user.length]=cpu_war2;
                user[user.length]=cpu_war3;
                user[user.length]=cpu_warcard;
                user[user.length]=cpu_card;
            } else {
                statement="The war resulted in a stalemate!";
                user[user.length]=user_war1;
                user[user.length]=user_war2;
                user[user.length]=user_war3;
                user[user.length]=user_warcard;
                user[user.length]=user_card;
                cpu[cpu.length]=cpu_war1;
                cpu[cpu.length]=cpu_war2;
                cpu[cpu.length]=cpu_war3;
                cpu[cpu.length]=cpu_warcard;
                cpu[cpu.length]=cpu_card;
            }
        }
        war();
    }
}
//When you are done, here it finds if you win or lose this game
 else if (user.length===52) {
    document.getElementByID("play").innerHTML="You have crushed your opponent.  Feel free to steal all of his belongings!";
} else {
    document.getElementByID("play").innerHTML="Unfortunatly, you have fallen victim to your opponent's wrath and have been conquered.;
}
}
        //-->
        </script>
    </body>