Edit in JSFiddle

/** Constructor with parameters
 * Make sure, the outputSpanID of two different instances
 * is not the same. Otherwise unpleasant things may happen.
 */
function Timer(count, interval) {
    this.count = count ? count : 0;
    this.interval = interval ? interval : 0;
    this.isPaused = false;
    this.intervalID = 0;
    this.outputSpanID = "time";
    this.callback = null;
}

// init function
Timer.prototype.init = function() {
    this.alert();
};

// alert the properties
Timer.prototype.alert = function() {
    alert(this.count + ":" + this.interval + ":" + this.isPaused + ":" + this.intervalID);
};

// print time
Timer.prototype.printTime = function() {
    document.getElementById(this.outputSpanID).innerHTML = this.count;
};

// start the timer
Timer.prototype.start = function(e) {

    //clear interval
    if (this.intervalID != 0) {
        clearInterval(this.intervalID);
    }

    //print time
    this.printTime();

    var self = this;

    //setInterval method sets the interval for repeating the function
    this.intervalID = setInterval(function() {
        self.count -= 1;
        if (self.count >= 0) {
            self.printTime();
        } else {
            self.stop();
        }
    }, self.interval);
};

// stop timer
Timer.prototype.stop = function() {
    //this.alert();
    clearInterval(this.intervalID);
    this.count = 0;
    this.interval = 0;
    this.isPaused = false;
    this.printTime();
    if(this.callback) {
        this.callback();
    }
};

// pause timer
Timer.prototype.pause = function() {
    //this.alert();
    clearInterval(this.intervalID);
    this.isPaused = true;
};

// unpause timer
Timer.prototype.unpause = function(e) {
    //this.alert();
    this.start();
    this.isPaused = false;
};

/**
 * init method
 */
function init() {

    var timer2 = new Timer(100, 1000);
    timer2.outputSpanID = "time2";
    //timer2.init();
    timer2.start();

    // get new instance of timer
    var timer = new Timer();
    timer.outputSpanID = "time";

    /* get the buttons and attach eventhandlers */
    var startBtn = document.getElementById("startBtn");
    var pauseBtn = document.getElementById("pauseBtn");
    var stopBtn = document.getElementById("stopBtn");

    startBtn.onclick = function() {
        timer.count = document.getElementById("timeBox").value;
        timer.interval = 1000;
        timer.start();
        if (timer.isPaused === true) {
            pauseBtn.innerHTML = "pause";
        }
    };

    pauseBtn.onclick = function() {
        if (timer.isPaused === false) {
            timer.pause();
            this.innerHTML = "unpause";
        } else {
            timer.unpause();
            this.innerHTML = "pause";
        }
    };

    stopBtn.onclick = function() {
        timer.stop();
    };
}

window.onload = init;

<form name="timeform">
<p>
    Time remaining: <span id="time">0</span>
</p>
<p>
    Time2 remaining: <span id="time2">0</span>
</p>
    
<p>
    <input type="text" id="timeBox" value=0 />
</p>
<br/>
        <button type="button" id="startBtn">Start</button>
        <button type="button" id="pauseBtn">pause</button>    
        <button type="button" id="stopBtn">Stop</button>
</form>

#time{font-size:2em; font-weight:bold}