how to get the value of list field type (check boxes)
Where do you put this PHP code? If it's in the page.tpl.php, then you can use the $logovariable to display the field or not.

Otherwise, this configuration is available in your theme. So you need to get your theme configuration, with theme_get_setting. You should have a variable 'toggle_logo' or something like this. The full code would be

$test = theme_get_setting("toggle_logo");
if($test) {
   //Put your code here
}


If you're using different theme, or you need to get this value for a specific theme, then you need to pass your theme name as second parameter of the function, for example:

$test = theme_get_setting("toggle_logo", "my_custom_theme");


[EDIT FULL ANSWER]

So you just need to check the value of the field field_options_site_logo before outputing the image:

$node=node_load(18);
if(isset($node-&gt;field_options_site_logo['und'][0]['value']) &amp;&amp; $node-&gt;field_options_site_logo['und'][0]['value'] == 'yes') {
  $logo_img = file_create_url($node-&gt;field_site_logo[$node-&gt;language][0]['uri']); //origional image path
  $show_logo = $node-&gt;field_options_site_logo['value']; //original image path
  if(isset($logo_img)) {
    $web_logo = theme('image_style', array('path' =&gt; $node-&gt;field_site_logo[$node-&gt;language][0]['uri'], 'style_name' =&gt; 'site_logo'));
    print $web_logo;
  }
}