WooCommerce is an e-commerce plugin and although it offers a great deal of filter hooks, function calls and theme support it’s not technically a theme framework.
Generally speaking WooCommerce will work with just about any theme right out of the box. But it does support customizing it’s own pages/layout by copying it’s files to the theme folder. You can find the docs here at WooThemes.com.
If you need to do more than than that check out the API documentation here.
As with customizing any plugin/theme there are standard/best practices you should follow. Generally speaking you never want to directly edit files within the plugin/theme. These would normally be overwritten any time you updated the plugin/theme.
For themes you’d want to build a custom theme that adds your functionality/layout on top of and existing theme. Check the ‘child theme’ for best practices, guidelines, and layout.
To modify a plugin (i.e. WooCommerce) you’d either want to make changes within your own theme, child theme, or a custom plugin. Again that way you don’t run the risk of your changes being over written when the plugin is updated.