I have both a WooThemes theme and the WooCommerce plugin:
For WooThemes themes, there's the ability to add Google Analytics tracking to the page in the General Settings:
"Paste your Google Analytics (or other) tracking code here. This will be added into the footer template of your theme."
It's also in WooCommerce:
Settings -> Integration Tab -> Google Analytics ID
Should I set it in both places, or only the WooCommerce one?