Magento – Use layered navigation attribute filter only in specific categories

You will only be able to do this hardcoded.

So filtering out the manufacturer and category on the left side and creating a custom PHTML file that generates links/dropdowns for the manufacturer and category in the center.

so in app/design/frontend/[template]/[package]/template/catalog/layer/view.phtml around line 49 edit

<?php if($_filter->getItemsCount() && ($_filter->getName()!='manufacturer' || $_filter->getName()!='categories')): ?>
   <dt><?php echo $this->__($_filter->getName()) ?></dt>
   <dd><?php echo $_filter->getHtml() ?></dd>
<?php endif; ?>

Would eliminate manufacturer and categories from the list. Optionally try to use getCode, I think that would return the attribute_code instead of the name.

For your center layered navigation create a new PHTML file and add it to the layout

<reference name="content">
   <block type="core/template" name="center_layered_nav" template="catalog/layer/center.phtml"/>
</reference>

and in the file catalog/layer/center.phtml something like this

<form method="GET" id="center_layered">
<select name="manufacturer" onchange="document.getElementById('center_layered').submit();">
<?php 
$attribute = Mage::getSingleton('eav/config')->getAttribute('catalog_product', 'manufacturer');

$options = $attribute->getSource()->getAllOptions(false);
foreach ($options as $option)
{
   echo '<option value="'.$option['value'].'">'.$option['label'].'</option>';
}
?>
</select>
</form>

when a user selects a manufacturer it should add manufacturer to the layered navigation URL. Manufacturer does have to be a filterable attribute tho.

This is highly untested code so may need a tweak or two but it's basically what you need. And I'm in no way pretending this is best practice but as far as I know it's the only way to do it.

edit the file /app/design/frontend/{package}/{theme}/template/catalog/layer/view.phtml and replace this line:

 <?php if($_filter->getItemsCount()): ?>  

with

 <?php if($_filter->getItemsCount() > 1): ?>

I only see one problem with this approach.
If all your filters have only one option they you will still get the section title

<p class="block-subtitle"><?php echo $this->__('Shopping Options') ?></p>

But this can easily be overcome if you loop through the available filters and see if you have at least one that has the items count bigger than 1.