Amanda,
Google Shopping is all handled through Google AdWords, Merchant Center and Analytics. Set up and optimization cannot be done outside of any of them.
There have been some issues brought up in the past about the Shopify Google Shopping App and some functionality errors.
I need a lot more information about your current account status to be of further assistance. If you'd like a free set-up for Google Shopping we would be happy to help you out and show you how to use it in the long run.
Chances are a lot of product data optimization will have to take place alongside helping you understand the CPC bidding system and how to profit over time against ad spend.
