Ecommerce theme from scratch using woocommerce

Hi, I seriously need somebody’s help!
I’m creating an ecommerce theme from scratch using php, css & html.
The problem I’m having is integrating into it woocommerce. I don’t know if I need to integrate code into the index.php, style.php, or template.php. Or even what code to type in!
I’ve downloaded woocommerce but right now its just sitting beside my wordpress site.
Does anybody have some insight into this that can help me please!?
Thanks!