Hey - I should have updated this thread already, I worked it all out today :) Let me explain what's going on as best I can (apologies in advance for the long read but hopefully it'll help).
I'm using the Modernize theme from Goodlayers which isn't Woocommerce compatible out of the box, so I had to make a few changes. One of these was to create a new template called woocommerce.php which contained code from my theme's page.php template, adjusted here and there. Someone else had done the hard work for me here already and this made most of the pages work with Woocommerce OK.
However, my current filtering is done using the Query Multiple Taxonomies plugin. The sidebar widget allows me to query the Product Attributes from Woocommerce automatically which is really nice, but I found the search results pages were all messed up and I was struggling with how to get them looking right. URL strings that worked from product cats were fine, product attributes not so.
I then read on another thread somewhere that I needed to take a copy of the taxonomy-product_cat.php file, rename it to match the new attribute(s) like this 'taxonomy-pa_myattributenamehere.php' and then add it to my theme folder.
However, the original taxonomy-product_cat.php file just contained code that called 'product-archive.php' and at first, I didn't know any different/better so used that same code in my new templates but it didn't work. I realised that it needed to be calling another template, or containing different code, but I wasn't sure what or how.
Today I worked out that these new taxonomy-pa_attributenamehere.php templates actually needed the same code as that I created for the woocommerce.php file, as this is the code that allows my theme to play nicely with Woocommerce. So today I just copied the code from my woocommerce.php template I created for my theme into these new taxonomy templates, which then went into the root of my theme folder alongside woocommerce.php.
Job done! Now I have a 3rd party theme, tightly integrated with woocommerce and some nice filtering to boot. Happy days. It's fairly close to Woo's Layered Nav widget, with the added bonus of working site wide, not just the Shop page etc.
Does that help? I can dig out some extra links if you need it.