Magento 1.9 – Create Different Attribute Sets for Categories

There is no direct connection to the "Custom Options" in a product and an attribute. You would have to simulate this manually. Follow these steps to do that:

Lets say you have a Category called Electronics. And an Attribute Set called Electronics.

Create a new attribute called whatever your Custom Option is, such as Extended Warranty.

When creating the Attribute, under Attribute Properties set Catalog Input Type for Store Owner and select either Dropdown, Multiple Select, or Price. Those are the only ones usable for filterable search.

Then in Frontend Properties select "Use In Layered Navigation".

Then click Manage Label/Options and input the options you would have in the Custom Options of the product.

Add this Attribute to the Electronics Attribute Set.

If you selected Dropdown as Catalog Input Type for Store Owner, then do the same for your Custom Options in the product. So if you had an Electronic, it now has the dropdown attribute for Extended Warranty or whatever attribute you want to use.

In the same module that you used for special price (explained here) you can add you attribute set also.
Just add this to the collection init ->addAttributeToSelect('attribute_set_id') and the corresponding column in _prepareColumns().

$sets = Mage::getResourceModel('eav/entity_attribute_set_collection')
            ->setEntityTypeFilter(Mage::getModel('catalog/product')->getResource()->getTypeId())
            ->load()
            ->toOptionHash();
    $this->addColumnAfter('set_name',
        array(
            'header'=> Mage::helper('catalog')->__('Attrib. Set Name'),
            'width' => '100px',
            'index' => 'attribute_set_id',
            'type'  => 'options',
            'options' => $sets,
    ), 'name');