I figured out the category listing issue. It’s in categories.xml. I just didn’t understand that everything was in there. I had the left nav in both the default page left column and the category listing left column. So it was showing it twice.
I still don’t understand how to customize my link structure. I can’t get a link like http://www.store.com/collections/mens/ to work. but http://www.store.com/collections-mens.html will work fine.
Some help please. Nobody seems to answer these forums. Or maybe people just don’t like me.