As you will soon discover, WooCommerce is an amazing solution for ecommerce and is the best WordPress option out there. However, unless a you buy or use a free WooCommerce theme, you will a completely optimized experience. I have experienced this problem many times. So, to get WooCommerce to match your theme:
WooCommerce is great but it is really difficult to get it to match your theme. The best thing you can do is get a subdomain for your site. Something like:
You can install a free WooCommerce theme onto the subdomain and link to it from your site's nav bar. Now you can at least have a blank WooCommerce theme.
It may sound like a hassle, and I know that you desperately want your store on your site but trust me, it is really hard to get the theme to match and this subdomain is the best option. I would by a WooCommerce theme but they usually do not match what I am trying to do, so I just love getting a WordPress theme that I like and then just linking to a subdomain.
Try this, you'll be glad you did!