PHP - Control Problem Based On Two Forms

Below is the screenshots and script for user page level access i have used it for one of my old projects. Code is working as it was intended. But it needs to be improvised.

Users table

pages table , which has all the pages and links

Access level table. which has user id from users table and page id from pages table (for which user has access)

Once the user is created, admin gives access to the user on page basis, the permissions.php page looks like this

The modules

Menus inside the modules

Pages in each menu

Here is my code for permission.php

<div id="demo2-html">                    
<ul id="demo2" class="mnav">
	<li><a href="#">Sales</a>
    <ul>
    <li><a href="#">Lead</a>
    <ul>
			<table class="table table-bordered table-striped table-hover">
				
                <?php 
				
				$s1 = mysqli_query($con, "SELECT pages.page_id as pid, pages.code, pages.page, 
									pages.href, access_level.aid, access_level.page_id as pgid, 
									access_level.user_id 
								FROM pages
								LEFT JOIN access_level ON (pages.page_id=access_level.page_id 
									AND access_level.user_id=".$user." 
									) WHERE pages.code='led'") or die(mysqli_error($con));
									
				while($s2 = mysqli_fetch_array($s1)) {  ?>
				<tr><li><td><?php echo $s2['page']; ?>  </td><td><input type="checkbox" name="sn[]" value="<?php echo $s2['pid']; ?>" <?php if($s2['pgid'] === $s2['pid']) echo 'checked="checked"';?> />
                <input type="hidden" value="<?php echo $s2['pid']; ?>" name="page_id[<?php echo $s2['pgid']; ?>]">
                </td></li></tr>
                <?php } ?>
                </table>
				</ul>
			</li>
            
            <li><a href="#">Customer</a>
    <ul>
			
			<table class="table table-bordered table-striped table-hover">
				
                <?php 
				
				$s1 = mysqli_query($con, "SELECT pages.page_id as pid, pages.code, pages.page, 
									pages.href, access_level.aid, access_level.page_id as pgid, 
									access_level.user_id 
								FROM pages
								LEFT JOIN access_level ON (pages.page_id=access_level.page_id 
									AND access_level.user_id=".$user." 
									) WHERE pages.code='cst'") or die(mysqli_error($con));
									
				while($s2 = mysqli_fetch_array($s1)) {  ?>
				<tr><li><td><?php echo $s2['page']; ?>  </td><td><input type="checkbox" name="sn[]" value="<?php echo $s2['pid']; ?>" <?php if($s2['pgid'] === $s2['pid']) echo 'checked="checked"';?> />
                <input type="hidden" value="<?php echo $s2['pid']; ?>" name="page_id[<?php echo $s2['pgid']; ?>]">
                </td></li></tr>
                <?php } ?>
                </table>
				</ul>
			</li>
      //code goes for all the other modules
      
      </ul>
            </li>
            
    
    
</ul>
</div>


<input type="hidden" name="user" value="<?php echo $user; ?>" />
<div class="row" align="center">
<input type="submit" name="submit" class="btn btn-success" value="Save" />
  </form> 



// form Submission

if(isset($_POST['submit']))
{
	$user = $_POST['user'];
	
 $sql = "DELETE FROM access_level WHERE user_id = ".$user."";
 $query = mysqli_query($con, $sql) or die (mysqli_error($con));

foreach($_POST['sn'] as $sn)
{
 $sql = "insert into access_level (page_id, user_id) values (".$sn.", ".$user.")";
 $query = mysqli_query($con, $sql) or die (mysqli_error($con));
}


if($query)
{
header("location:users.php?access=1");	
}

	
}
  

So against each user i am storing all the page ids here. When i edit any of the users, it deletes all the records and again insers new records. Which i feel is not a proper way to do.
And also, if i have 10 users and 100 pages, suppose all the users are having access to all the pages, records in user_access table will be 1000. 

And in codewise also, i am redirecting the user to no_access.php (as below) page if the user do not have access.

<?php
ob_start();
include("connect.php");
include("admin_auth.php"); 
$q1 =  basename($_SERVER['REQUEST_URI'], '?' . $_SERVER['QUERY_STRING']);
$q2 = $_SERVER['REQUEST_URI'];
$var1 = "/".$q1;

$qa_path=explode('/', $q2);

$right_path = $qa_path[2].$var1;

$parsedUrl = parse_url($q2);


$curdir = dirname($_SERVER['REQUEST_URI'])."/";



$m4 = "select p.page_id, p.code, p.page, p.href, al.aid, al.page_id, al.user_id FROM pages p INNER JOIN access_level al ON p.page_id=al.page_id WHERE al.user_id=".$_SESSION['user_id']."";

$m5 = mysqli_query($con, $m4)  or die (mysqli_error($con));


while($nk1 = mysqli_fetch_array($m5)) {
	
	$href1[] = ($nk1['href']); }
	
	
	if(in_array($right_path, $href1)) {

echo "<script type='text/javascript'> document.location = ".BASE_URL."/".$right_path."</script>"; 
}
else
{

echo "<script type='text/javascript'> document.location = '../no_access.php' </script>";
exit();
}	

?>

I need help in improve and better/effective (structural) way to do this both in database and php script. 

<!DOCTYPE html>
<html>
<body>
   <!-- processDomains.php is this file - it calls itself (for testing purposes so I can see what is happening) -->
   <form action="processDomains.php" method="post">
   <?php
       // create the domains array (there are actually several entries in the array but I cut it down for testing)
       $domains = array (1 => 'Decommission', 'Migration');
    
       echo "Select Domain:";
       echo "<br>";
    
       // Make the domain pull-down menu - this displays correctly
       echo '<select name="domain">';
       foreach ($domains as $key => $value) {
          echo "<option value=\"$key\">$value</option>\n";
       }
       echo '</select>';

       // input doesn't matter what is 'submitted', always goes to last $value
       echo '<input type="submit" name="submit" value="Submit">';

       // call function subdomains
       subdomains ($value);
    
       function subdomains ($domains) {
           // define values for each array - each array contains available choices for the subdomain pulldown menu
           $migration = array (1 => 'Application Migration', 'Application Patch', 'Application Upgrade');
           $decommission = array (1 => 'Applications', 'Servers', 'Storage');
    
           if ($domains === 'Migration') {
              echo "Select subdomain:";
              echo "<br>";
              // Make the Migration pull-down menu
              echo '<select name="migration">';
              foreach ($migration as $key => $value) {
                  echo "<option value=\"$key\">$value</option>\n";
              }
              echo '</select>';
           } else if ($domains === 'Decommission') {

              /* ===
               * since 'Decommission' is the last entry in the 'Domains' pulldown list, $value ALWAYS equals
               * 'Decommission' and $domains equals $value. So this menu SHOULD work but is always
               * empty.  Thus, two problems - the pulldown menu is always empty and $value isn't based
               * upon user input.
              */
              echo "Select subdomain:";  // this prints so I know I'm in 'Decommission (I eliminated the echo "$domain" to show I'm always coming here)'
              echo "<br>";
              // Make the 'Decommission' pull-down menu
              echo '<select name="decommission">';
              foreach ($decommission as $key => $value) {
                  echo "<option value=\"$key\">$value</option>\n";
              }
              echo '</select>';
              echo '<input type="submit" name="submit" value="Submit">'
           ) // end of 'if-else'
    } // end of function 'subdomain'
     
?>
</form>
</body>
</html>