1. make a "logged_time" column somewhere in your database (I put this in my users table)

2. When your users log in do something like this in your login script:
<code lang="PHP">
<?php
$_SESSION['user_id'] = $userid;
$_SESSION['online_time'] = mktime();
?>
</code>

3. On the top of each page...or in your header file have this:
<code lang="PHP">
<?php
if(getUser()){ //<- this checks to see if the user is logged on...you can do this anyway you want
onlineTime(); //<- this alters/saves the online time
}
?>
</code>

4. Here are your main functions:
<code lang="PHP">
<?php 

//This function logs the time into the database and makes a new time
function onlineTime(){
	//Make DB connection here
	
	$timeout = 5; //this is the timout in minutes
	
	$userid = $_SESSION['user_id'];
	
	$now = time();
	$difference = $now - $_SESSION['online_time'];
	if($difference <= ($timeout * 60)){
		mysql_query("UPDATE users SET logged_time = logged_time + $difference WHERE userid = $userid");
	}
	$_SESSION['online_time'] = mktime();
}

//This function calculates and outputs the logged time
function showOnlineTime($userid){
	//Make DB connection here
	
	$result = mysql_query("SELECT logged_time FROM users WHERE userid = $userid");
	if(mysql_num_rows($result) > 0){
		list($total) = mysql_fetch_row($result);
		$days = floor($total / 86400);
		$hours = floor(($total % 86400) / 3600);
		$minutes = floor(($total % 3600) / 60);
		echo "$days days, $hours hours and $minutes minutes.";
	}else{
		echo "No Logged Time Available";
	}
}

?>
</code>

To output the information all you have to do is this:
<code lang="PHP">
<?php
$userid = 5;
showOnlineTime($userid);
?>
</code>